1. Healthcare practitioners’ primary obligations are towards their patients, not towards their own personal conscience. When the patient’s wellbeing (or best interest, or health) is at stake, healthcare practitioners’ professional obligations should normally take priority over their personal moral or religious views.
There are a number of things very notable about the structure of this claim, each of which involves something at least highly controversial.
(1) It opposes professional obligation to obligations of conscience as if they were different rather than overlapping things. But conscience is historically understood as that whereby we discern and judge what our obligations are in a given case in the first place, so a question arises as to how one can have a full account of professional obligation without taking professional obligation also to include at least high-level obligations about acting on your conscience. Surely it's a professional obligation to act conscientiously toward one's patients? And if not, why would one take professional obligations generally to take priority over acting conscientiously?
(2) It orders obligations without examining their content. How is it even possible to do that? A look at a different kind of case might help highlight the issue here. If we take the most discussed cousin of this kind of obligational conflict, the case of a priest and the seal of the confessional (for which there are entire tomes of discussion spanning centuries), the 'professional obligation' is taken to override obligation of conscience only because the 'professional obligation' to uphold the seal of the confessional is taken to be divine law instituted for the salvation of souls, so that if your conscience tells you to do otherwise, your conscience is guaranteed to be wrong. Because of this, one has a moral obligation to make sure that one's conscience doesn't tell one otherwise, and a moral obligation to uphold the seal of confession overrides the obligation to uphold one's conscience only because the latter is wrong in such a way that you are also morally obligated not to follow your conscience into error. But this kind of structure is unique to the case; it arises from the content of the obligation. Nobody claims a pharmacist's professional obligations are divine assessments incapable of being wrong, or that pharmacists have a moral obligation to form their conscience so that it never conflicts with their professional obligations.
(3) It assumes that it is possible to assess "wellbeing (or best interest, or health)" entirely independently of whether one is following one's conscience or not. The only possible argument that could be given for the priority of professional obligation over obligation of conscience is that this is somehow required for what is at stake -- in this case, apparently this vague and ill-defined good of "wellbeing (or best interest, or health)". But surely, whatever it may be, this good is not cordoned off from matters of morality? The wellbeing and best interest and, in a broad sense, health of patients seems to require that they be treated with at least a certain basic morality and decency by doctors who can be trusted to act conscientiously.
(4) It assumes that we can morally take external obligations to have priority over our best judgments about morality itself. Things can get a little complicated when we factor in our recognition that we can be wrong, but one's personal moral views are precisely what one takes morality to be, to one's best estimate. How can anyone morally take something inconsistent with morality to have priority over what in your best judgment is morality?
(5) It assumes that there is a well-defined body of professional obligation. Obviously there will be families of things that come up. But, for instance, why should we consider one's professional obligation as a doctor, generically considered, and not (say) one's professional obligation as an American doctor, or one's professional obligation as a Catholic doctor, or one's professional obligation as a doctor participating in the local community, or one's professional obligation as a decent and morally upstanding doctor, to be the right way of grouping the obligations? This is related to (2), but deals with a serious problem -- it assumes that "personal" (it seems really to mean 'private') views do not qualify your profession. But when we are dealing with religion and morality, this is surely at least highly controversial.
(6) How do we get professional obligations in the first place, if not by starting with obligations of conscience of actual doctors and abstracting? What makes something a genuine professional obligation? This is surely relevant to the question of whether such an obligation overrides what people think is moral?
We can also see the problem by looking at a different kind of case. A citizen's primary obligation is to uphold the good of society; so, one might say, when matters important to society are involved, one's obligations as a citizen should normally take priority over one's moral and religious views. But one's obligations as citizen include maintaining a society in which people can, to the extent possible, fulfill their moral and religious obligations as best they can. Someone consistently sacrificing their conscience to civic obligation is not actually acting as a good citizen. Many of our civic obligations are extrinsic and positive -- they are not, in and of themselves, required for moral living, but only for convenience and smooth functioning of society. So one wouldn't expect to be able to make a general claim about what obligations take priority without looking at the specifics of the obligations. The good upheld by one's civic obligations cannot be completely assessed, nor requirements for it completely determined, without considering the goods protected by obligations of conscience. No civic obligation can take priority over morality itself, so if a civic obligation conflict with your best assessment of what is morally obligatory, you have a moral obligation to violate the civic obligation, not a moral obligation to violate the moral obligation. And our civic responsibilities are not generic; our obligations are not merely those of citizens considered generically but conscientious citizens, Catholic citizens, Jewish citizens, citizens participating in particular communities. So the analogue of (1) doesn't seem to make much sense for civic obligations -- but many civic obligations are far more serious and important, as obligations, than many and probably most professional obligations.
There are other problems with the statement. One that is especially serious is its later emphasis on sincerity (which it's getting from the fact that it has become common to smuggle the concept into various laws):
4....The burden of proof to demonstrate the reasonability and the sincerity of the objection should be on the healthcare practitioners.
5. Accordingly, in such countries, the reasons healthcare practitioners offer for their conscientious objection could be assessed by tribunals, which could test the sincerity, strength and the reasonability of healthcare practitioners’ moral objections to certain medical services.
It makes sense to require conscientious objectors to state (as point (3) demands) why, exactly, they are objecting; but if your conscientious objection protections depend on being able to sort out the sincere from the hypocritical in general, you are not really protecting conscientious objection. How does one actually prove sincerity? Beyond continuing to insist on something even in the face of negative consequences, you can't. It's a matter of subjective motivation, and anything a sincere person can do, a hypocrite can also do -- even in the case of negative consequences, we are reasoning that a hypocrite wouldn't be motivated to continue the hypocrisy, not that a hypocrite couldn't endure those negative consequences if they thought they still could get something out of it.
Thus we can't be talking about real sincerity; tribunals are not competent at assessing real sincerity. In practice, when sincerity comes up in law, what courts really look at are history and consistency. This will obviously lead to some sincere cases being treated as 'insincere' -- for instance, if I have only recently had the moral epiphany leading to my conscientious objection and I am still sorting out what the implications of it, which is not a so very uncommon situation. And nice and sharp though 'consistency' might sound, it's a matter of degree here, because nobody is perfectly consistent in moral matters; that's one of the most blatantly obvious empirical facts about moral matters. And it's unclear why consistency should be an issue, anyway -- for instance, if someone is an inconsistent backsliding member of a religious community whose moral objection to blood transfusions is well known, why isn't their membership in that community in and of itself sufficient? It's obviously relevant; conscientious objection is not, contrary to the way the statement phrases it a matter of "personal" moral views but a matter of participating in a moral community as a member of a moral community. This may or may not have a religious tinge, but membership in a community that voices a moral objection, regardless of personal consistency with that moral principle, is sufficient to establish that the person in question is not simply making up the objection, and to establish that there is a real moral issue here. Obligations of conscience are not merely private or personal; they are things that can be shared by participation in a community.
Another issue that comes up:
7. Healthcare practitioners who are exempted from performing certain medical procedures on conscientious grounds should be required to compensate society and the health system for their failure to fulfil their professional obligations by providing public-benefitting services.
Here again we have the assumption that you can actually have a professional obligation to violate what seems to be your moral obligations. This misses the entire point of protecting conscientious objectors of any kind, which is that conscientious objectors are sometimes the ones who are right about the state of obligation, and that even when they aren't, they have an obligation to put moral obligations above other obligations. Conscientious objection is not civil disobedience unless it is prohibited; it is a protected right because there is something very important about it for society. People who conscientiously object are doing what they should be doing -- as citizens, certainly, and, yes, as professionals. They aren't doing anything wrong that requires compensation. Yes, it's fairly standard for conscientious objectors to do other things (for instance, a conscientious objector to fighting in a war might instead fulfill his civic obligations by serving in the cafeteria or as a janitor), but this is not 'compensation' for 'failure to fulfil one's obligations' -- it's a way of fulfilling those obligations in a more morally acceptable way.
Even if we did confine ourselves to talking about conscientious objection in matters where it involves civil disobedience, this kind of idea is absurd. If someone conscientiously objected over a fugitive slave law, refusing to turn over a runaway slave due to moral objections, we might call this 'failure to fulfil their legal obligations', but we could just as easily say that they haven't failed to fulfill their legal obligations at all, because no one can be legally obligated to do what is morally evil. The statement is sneaky about it, but in fact it keeps smuggling into its claims a controvertible theory of obligation -- one in which obligations can conflict, one in which you can have immoral obligations. The conscientious objector in the fugitive slave case does not actually need to 'compensate' us for refusing to do it. We might settle on some such compensation as a compromise deal, but if they are morally in the right, we owe them something because we're the ones harassing them for doing the right thing, not they us. I mean, seriously, take the provisions of this statement and apply it to conscientious objection of citizens in racial matters -- conscientious objection in enforcing segregation laws, for instance. The analogues of the statement in such a situation would often be morally atrocious. The legal system should be getting the matter right in the first place, or, failing that, taking into account the possibility that it is not getting it right, not sanctioning those who refuse to go along with what they see as evil or wrong.
Just as all citizens by the very nature of citizenship have a civic obligation to recognize that there are higher things than the laws of a society, and that these laws themselves must be subject to moral standards, so all professionals in any profession have a professional obligation to make sure that their standards of professional ethics are consistent with higher moral standards. If we were all angels, this might be easy enough. Human beings, however, sometimes misjudge in creating standards of professional ethics, just as they do in making laws or in enforcing customs, and these standards, even when right, will not capture everything important, or even everything essential, just as laws don't capture everything important or even essential about a society. Because of this, we allow room in controversial matters for conscientious objection, whether it be in our legal system or in our standards of professional ethics, and if we are not complete idiots, we will allow explicit room for it. Conscientious objection, according to any sensible standard of professional ethics, is not a violation of professional ethics, but a fundamental part of professional ethics. Any account of professional ethics that does not clearly recognize this is defective at its core.