The question itself would be meaningless, as the circumstances surrounding each man and the society he is a part of, already pretty much makes it clear that a certain course of action will be taken against a "bad man", despite possible loss of innocent lives, according to the graveness of the situation. Therefore, the attempt to distingush one death to another, is actually an attempt to justify the aftermath of a course of action that may have led to someone's death, and therefore, is immoral from the very start.
In other words, "questions" are only meaningful if an answer to that certain question may actually change the final outcome. However, in many cases (such as war, or perhaps policemen engaged in a gunfight against criminals) the outcome is already decided: there is no averting the fact that people will be orderd/forced/compelled to kill someone else, whether or not they have any personal moral conflicts inside them. The very situation surrounding them destroys the normal barriers of morality a society holds.
Thus, before one draws any answers upon facing that very question, one must first decide what they are willing to do about it, if the answer to that question is something their morality cannot accept.
For instance, you have been assigned to a death squad. You have been ordered to kill innocent people. You feel conflicted whether you should follow the order or not. Under these circumstances, asking oneself "is it right to kill these people or not" is meaningless. The only question that has any meaning is, "am I going to pull the trigger and kill these people or not". The odds are, you will probably pull the trigger anyway, and any question on whether it was right to kill or not, becomes nothing but a series of mental masturbations to somehow justify oneself and feel comfortable about it.
That, is what the question is about.
