And so too for atrocities in war. The non-zero number of atrocities in no way suggests that people just blindly follow orders, as a matter of fact. You need to compare these numbers to what would happen if people gave no consideration to morality whatsoever in their execution of orders. And what are those numbers? I'm not sure, but I expect vastly higher than the relatively few atrocities we can reference.
We see this sort of attitude when it comes to discussions of police brutality. Many police officers view the use of lethal force through the lens of self-defense in high stakes scenarios. Others view the use of lethal force through the lens of "police are not judge, jury, and executioner".
When people get shot as they run away from the police, even if each side of the debate might be rational in their own world-view, the conclusions are completely opposed.
The disconnect, I believe, is what one considers duty another may consider blind faith. There is a vast amount of room for ambiguity here.
None of this will be declassified for years, it's technically still not over yet, we'll be waiting a long time to know some of the things we still don't know now.
There is a point at which we have to consider whether war is worth the atrocity. What is so important that entire civilizations would condone the slaughter of their 'enemies'?
I have some of my own opinions on the above question, I only ask because I think the question should be considered carefully.