The Justice of the War does matter
"As you likely realized while reading the bubble theory, its approach to justifying killing in war requires that the soldier be fighting for a war that is just. This is a stumbling block for many military professionals. The bubble theory rejects the long-held tenet of the Just-War Tradition that soldiers on both sides of a war are “moral equals”—equally innocent of responsibility for the war but equally guilty of threatening each other. This claim of moral equality between unjust aggressor and just defender treats all soldiers as “innocent aggressors,” and thus reduces the “justification” of killing in war to the moral equivalent of gang warfare—no one is wrong because all are wrong, i.e., all soldiers have lost their bubbles. This waiver on soldiers’ responsibility for fighting may have had merit when feudal lords rounded up their serfs and led them into battle, but it does not reflect the educated, informed, morally autonomous citizen-soldiers of today.
We and our Soldiers cannot simply abdicate our responsibility to respect others’ human rights simply because we took an oath. Granted, given the huge responsibility we bear to protect the innocent, I do think that American Soldiers are morally obligated to fight unless they are convinced that a war is unjust. But I also think that an option should exist for selective conscientious objection. I doubt this would undermine good order and discipline. The patriots who volunteer to defend freedom will not abandon their fellow Soldiers without good cause. I have found most conscientious objectors to be woefully misinformed about morality in war. A healthy, ongoing conversation on the subject might actually enhance not only our Soldiers’ well being, but also recruiting and retention."