Each individual is a sovereign of his own will. Warfare is a clash of wills that involves coercion. Determining whether one is justly participating in warfare amounts to determining the rights violations occurring and who is instigating them.
In a war, rights of noncombatants are different from the rights of the soldiers, and not every enemy's act is deserving a military response. Thus the three points Aquinas made about the need for civil leadership in a just war pertain to individual rights and are not mere prudence. His "sovereign" is one who can make a judgement and take on the responsibility for potential war crimes as he dispatches the soldiers to kill people and break things. 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.