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?
In the former case justification for war matters. Compare moral effect of Perl Harbour and compare that to war in Vietnam.
Same army will be far more motivated to fight to defend the homeland than to kill a poor sod in a faraway land for unclear reason. So it's not a static quality.
And every time there is a fuckup from the higher ups it affects morale.
Take it to the extreme, and you have nazi atrocities and 'just following orders'.