The pernicious effect of religion here is more than just on the children of parents who follow specific religions that may find vaccines objectionable (which, by the way are few in number). In this case, religion gives cover to parents who just don't want to vaccinate because of pseudoscientific fear-mongering or "philosophy." Undue respect for religious beliefs that clash with the scientifically proven ability of vaccines to prevent disease safely enables these parents to easily bypass vaccination laws. With an increasing number of states providing more and more religious and "philosophical" exemptions to vaccines, I fear that it will only be a matter of time before diseases once thought vanquished return in a big way on these shores.
Now, Orac is a doctor -- a surgical oncologist, if I remember correctly -- so it is not the least surprising that he gets worked up about this, and quite rightly, too. But I don't think this is quite the right way to put it. In part this is because 'giving cover to liars' is not a pernicious effect of anything; quacks appeal to science as a cover for their cons; it does not follow that quackery is a pernicious effect of science. As Orac notes, in twenty states in the U.S. you don't even need a medical or religious reason to get an exemption; a 'philosophical one' will do. This is not a case of philosophy having a pernicious effect of giving cover to antivaccination; it is a case of a law written so that a 'philosophical exemption' just becomes an exemption anyone can get without having to do anything to prove that they really have a serious philosophical reason for not vaccinating their children. The primary problem in these religious cases is clearly that there is no system of accountability in place to guarantee that religious exemptions serve the function of protecting religious freedom. As Orac notes, very few religious groups actually have an anti-vaccination stance; it has been noted in a number of surveys that most religious groups tend to be favorable toward vaccination, with Church of Christ Scientist being the major exception. Moreover, it is incorrect to say that the religious beliefs "clash" with the scientifically proven abilities of vaccines; unless the religious beliefs are that the vaccines don't work, which is also going to be rare, rather than (say) some view about what is required for the integrity of the body, there is no clash. Medical science is an instrumental discipline, not a normative one; it can't "clash" with a norm, however bad for health that norm may be. What is at stake here is a clash between personal moral opinion -- a community opinion in the rare genuine case of religious exemption, like that of the Christian Scientists -- and the general political and moral interest in a healthy populace.