Some important distinctions
First, there's the essential question. Is it ever morally justified to kill enemy combatants? If killing the bad guys is not morally justifiable, then all participation in war is immoral. I feel very confident that killing combatants who fight for an unjust cause is morally permissible and perhaps obligatory for soldiers waging a just war. In fact, I find that many people who oppose war on moral grounds don't have a problem with killing enemy combatants of an unjust aggressor.
What they they have a problem with is believing that the unjust enemy combatants can be held responsible for their actions. This leads to the question, Does it matter (morally) if the enemy combatants have been coerced (to some extent) into fighting? And what, after all, constitutes sufficient coercion to absolve a person of his moral responsibility?
Finally, there's the question of the unintentional killing of noncombatants. Even if it's morally permissible to kill the enemy combatants (free and coerced), should you do so if you can reasonably foresee that non-combatants will be killed as well?
In short, the issues of moral responsibility and collateral damage are central to almost all discussions about the morality of killing in war, although too often we don't make these distinctions explicit. I think that I make a good case for the morality of killing unjust enemy combatants, given that I hold myself (and others) to a high standard of autonomy and moral responsibility. The collateral damage piece I'm still trying to think, through. Our enemy in the current war uses noncombatants as tools to gain an advantage, so we cannot hope to avoid the issue.