Two nights ago I had a dream. I was in the military, and we were being deployed, and I suddenly got worried about something like this line of thought (I am filling in some details--it was more inchoate in the dream). I wasn't in a position to figure out on my own whether the particular actions I was going to be commanded to do are morally permissible. And these actions would include killing, and to kill permissibly one needs to be pretty confident that the killing is permissible. Moreover, only the leaders had in their possession sufficient information to make the judgment, so I would have to rely on their judgment. But I didn't actually trust the moral judgment of the leaders, particularly the president. My main reason in the dream for not trusting them was that the president is pro-choice, and someone whose moral judgment is so badly mistaken as to think that killing the unborn is permissible is not to be trusted in moral judgments relating to life and death. As a result, I refused to participate, accepting whatever penalties the military would impose. (I didn't get to find out what these were, as I woke up.)
Upon waking up and thinking this through, I wasn't so impressed by the particular reason for not trusting the leadership. A mistake about the morality of abortion may not be due to a mistake about the ethics of killing, but due to a mistake about the metaphysics of early human development, a mistake that shouldn't affect one's judgments about typical cases of wartime killing.
But the issue generalizes beyond abortion. In a pluralistic society, a random pair of people is likely to differ on many moral issues. The probability of disagreement will be lower when one of the persons is a member of a population that elected the other, but the probability of disagreement is still non-negligible. One worries that a significant percentage of soldiers have moral views that differ from those of the leadership to such a degree that if the soldiers had the same information as the leaders do, the soldiers would come to a different moral evaluation of whether the war and particular lethal acts in it are permissible. So any particular soldier who is legitimately confident of her moral views has reason to worry that she is being commanded things that are impermissible, unless she has good reason to think that her moral views align well with the leaders'. This seems to me to be a quite serious structural problem for military service in a pluralistic society, as well as a serious existential problem.
The particular problem here is not the more familiar one where the individual soldier actually evaluates the situation differently from her leaders. Rather, it arises from a particular way of solving the more familiar problem. Either the soldier has sufficient information by her lights to evaluate the situation or she does not. If she does, and she judges that the war or a lethal action is morally wrong, then of course conscience requires her to refuse, accepting any consequences for herself. Absent sufficient information, she needs to rely on her leaders. But here we have the problem above.
How to solve the problem? I don't know. One possibility is that even though there are wide disparities between moral systems, the particular judgments of these moral systems tend to agree on typical acts. Even though utilitarianism is wrong and Catholic ethics is right, the utilitarian and the Catholic moralist tend to agree about most particular cases that come up. Thus, for a typical action, a Catholic who hears the testimony of a well-informed utilitarian that an action is permissible can infer that the action is probably permissible. But war brings out differences between moral systems in a particularly vivid way. If bombing civilians in Hiroshima and Nagasaki is likely to get the emperor to surrender and save many lives, then the utilitarian is likely to say that the action is permissible while the Catholic will say it's mass murder.
It could, however, be that there are some heuristics that could be used by the soldier. If a war is against a clear aggressor, then perhaps the soldier should just trust the leadership to ensure that the other conditions (besides the justness of the cause) in the ius ad bellum conditions are met. If a lethal action does not result in disproportionate civilian deaths, then there is a good chance that the judgments of various moral systems will agree.
But what about cases where the heuristics don't apply? For instance, suppose that a Christian is ordered to drop a bomb on an area that appears to be primarily civilian, and no information is given. It could be that the leaders have discovered an important military installation in the area that needs to be destroyed, and that this is intelligence that cannot be disclosed to those who will carry out the bombing. But it could also be that the leaders want to terrorize the population into surrender or engage in retribution for enemy acts aimed at civilians. Given that there is a significant probability, even if it does not exceed 1/2, that the action is a case of mass murder rather than an act of just war, is it permissible to engage in the action? I don't know.
Perhaps knowledge of prevailing military ethical and legal doctrine can help in such cases. The Christian may know, for instance, that aiming at civilians is forbidden by that doctrine. In that case, as long as she has enough reason to think that the leadership actually obeys the doctrine, she might be justified in trusting in their judgment. This is, I suppose, an argument for militaries to make clear their ethical doctrines and the integrity of their officers. For if they don't, then there may be cases where too much disobedience of orders is called for.
I also don't know what probability of permissibility is needed for someone to permissibly engage in a killing.
I don't work in military ethics. So I really know very little about the above. It's just an ethical reflection occasioned by a dream...