I think those are two separate issues.

The former is about operational readiness. If your army is unable to shoot at the enemy for whatever reason, you don't have a functional army. Wars are lost because of this (which leads to political concessions and loss of resources/influence/etc), and it's an important topic to consider when your goal is to maintain a standing army like the US.

The latter is, well, morality.

Of course, these two topics clash. How far do you go to ensure an obedient and effective army, while allowing leeway to refuse orders that are immoral?