War is a clash of wills that involves coercion. The status of rights doesn't change because a war exists. All individuals also retain their rights during that war. The primary function of civil government during war remains the same as it is w/o being in a state of war. That's because in reality war always exists, it's just a matter of what intensity exists at any particular time, between whatever particular parties.
" Soldiers that make ethical determinations on their own will not be an effective fighting force and thus will violate the rights of their own citizens who delegated them to fight; soldiers that receive a blanket dispensation from the "Thou shalt not kill" commandment will violate the rights of noncombatant enemy."
Individuals are sovereigns of their own wills. If you're talking about a group that is waging a just war, then the individual participants retain their sovereignty of will. That means they make their own ethical decisions. They will make their own ethical decisions even if their is no war. If they make the wrong ones, it's a crime, but they still make their own decisions.
Commanders determine campaign strategies and announce goals and intents. Successful armies operate with only that much. Then their subordinates act on the commanders intent. US soldiers traditionally make their own ethical decisions. There have been very few problems with that, and they are certainly an effective fighting force.
Recall Senator Kerry's trepidation over his killing of civilians in Vietnam, reflecting the conflict between his individual conscience and duty as a soldier. In absence of a "sovereign's" decision on what to do with villagers that harbor Viet Cong that war would have been either not prosecutable at all, or it would have been a My Li style free for all, or some mixture of desertions and massacres depending on the temperament of the GI's involved. Aquinas says that no war can be just unless the right and wrong conduct is established centrally for all.