Andy,
Atrocities do happen, and often, at the level far above that of the foot soldier.
Bombing cities full of enemy civilians falls into this category for many. Personally, my mind is divided on this. On the one hand, it can be argued that targeting non-combatants is never right. On the other, it can be argued that these cogs make the machine run, and if they are unwilling to change their leadership, they are legitimately the enemy, as well.
From everything I've heard from the last century, it does appear to be easier to stay further removed from the harsh realities when you're pulling a lever on a machine thousands of feet from the target.
Seeing a live human without weapons over your rifle sights is a different matter, I think. I'm not sure which "smiley" face to add here.
Bad things happen in wars. Wars are part of the human condition. I wrote a very brief statement of goals for the grad school application I'm working on, a few hours ago. Here's part of it.
There is no algorithm to the human heart, but I feel that careful study of various aspects of military history can provide a convenient heuristic for better understanding a culture or people. Evolutionarily speaking, human conflict must serve a purpose, so it must be futile to imagine that any of us possesses the tools to abrogate such conflict entirely. What can certainly be done, is to understand why and how past conflict has occurred, so that future generations can be taught steps reasonably certain to reduce the likelihood of unnecessary conflict. This is my goal.
Your friend,
John