For me to choose to kill the innocent as a means to their ends is always murder, and murder is one of the worst of human actions. So the prohibition on deliberately killing prisoners of war or the civilian population is not like the Queensberry Rules: its force does not depend on its promulgation as part of positive law, written down, agreed upon, and adhered to by the parties concerned.
When I say that to choose to kill the innocent as a means to one's ends is murder, I am saying what would generally be accepted as correct. But I shall be asked for my definition of "the innocent". I will give it, but later. Here, it is not necessary; for with Hiroshima and Nagasaki we are not confronted with a borderline case. In the bombing of these cities it was certainly decided to kill the innocent as a means to an end. (p. 64)
For this reason she determinedly opposed Truman's honorary degree. She conceded that the bombs might have saved a large number of lives. But this is doing evil that good may come, and as she says, what that principle really means is: "every fool can be as much of a knave as suits him" (p. 65).
She was overwhelmingly voted down because the pro-degree people stacked the House. According to her, the dons at St. John's were told "The women are up to something in Convocation; we have to go and vote them down." At other colleges, absurd excuses were given, e.g., "It would be wrong to try to punish Mr. Truman." The speech at the ceremony was a tissue of equivocations: We don't approve the action; we think it was a mistake; but Truman didn't make the bombs; and he didn't decide to drop them without consulting anyone; he didn't do anything, in fact, except make the decision; hang it all, you can't hold a man responsible for making decisions! Anscombe's characterization of the speech is quite funny.
The second part of the paper takes an interesting turn; it is an argument that pacifist arguments are to blame for much of the failure to make the right distinctions in this sort of case. As she says,
It is characteristic nowadays to talk with horror of killing rathr than of murder, and hence, since in war you have committed yourself to killing--for example "accepted an evil"--not to mind whom you kill. This seems largely to be the work of the devil; but I also suspect that it is in part an effect of the existence of pacifism, as a doctrine which many people respect though they would not adopt it. This effect would not exist if people had a distinct notion of what makes pacifism a false doctrine. (p. 67)
In other words, because of the sloppy propaganda of pacifists, people come away with exactly the wrong lesson: they become dabblers in realpolitik. Because they themselves would never be pacifists, they resign themselves to becoming realists, and the reason is that pacifists try to break down the distinctions established by just war theory. This is not theoretical; she experienced quite a few cases of exactly this sort and, indeed, it's not difficult to find them today. So from Anscombe's point of view, refuting pacifism is actually not so much a twist as a natural development of Anscombe's protest against the sort of mass murder involved in the bombings and Hiroshima and Nagasaki. The pacifist who abhors any killing in war and the realist who will accept any killing in war are both engaged in a similar project: the pacifist turns every such killing into murder; the realist turns every such murder into something justified by necessity. Neither can admit a distinction of kinds; both the pacifist and the realist wish to show that all killing in war is just the same as murder. The only difference is that the pacifist wants to draw from it the conclusion that you should never kill, while the realist wants to draw from it the conclusion that sometimes you should regard yourself as forced to murder. The pacifist has much better propaganda; but realpolitik reaps more of the benefits of that propaganda than pacifism does. Realpolitik is just pacifism turned hypocritical. Her conclusion is very strong:
The correct answer to the statement that "war is evil" is that it is bad--for example a misfortunte--to be at war. And no doubt if two nations are at war at least one is unjust. But that does not show that it is wrong to fight or that if one does fight one can also commit murder.
Naturally my claim that pacifism is a very harmful doctrine is contingent on its being a false one. If it were a true doctrine, its encouragement of this nonsensical 'hypocrisy of the ideal standard' would not count against it. But given that it is false, I am inclined to think it is also very bad, unusually so for an idea which seems as it were to err on the noble side. (p. 70)
She ends by pointing out that her protest was not a protest of atomic weapons; people aren't murderous because they have atom bombs, they have atom bombs because they are murderous. What she objected to was their offering Truman honors, "because one can share in the guilt of a bad action by praise and flattery, as also by defending it" (p. 70).
G. E. M. Anscombe, "Mr Truman's Degree," The Collected Philosophical Papers of G. E. M. Anscombe, vol. III (Ethics, Religion and Politics). Blackwell (Oxford: 1981) 62-71.