Most people have a conscience, and there are usually some ideals we can all agree on, like love, justice and equality, at least in developed countries.
So, when people are recruited into the military, occasionally they are ordered to commit some sort of atrocious act.
In initial stages of the French revolution, when revolt broke out in Paris, the French troops sided with the civilians, because they realised what the National Assembly was trying to do for all Frenchmen.
In the beginning of the Russian revolution, when soldiers were ordered to fire into the crowd, the soldiers shot their officers instead.
From the above two events, we can establish that morality and individual thought still exists in soldiers of the military, so "I was just following orders" is a very poor excuse.
Now, however, we have always heard about some form of atrocities happening in wars, especially in the 20th century, and even nowadays.
In WWI, the Germans used those helium balloons to attack civilians in Britain. In WWII in China, the Japanese massacred millions of civilians and there was also that Rape of Nanking (which may have been exaggerated through propaganda but it still was an event). We all know about the holocaust, which was carried out by German soldiers. Even in recent days we've heard news about the USA using drones to bomb buildings suspected of harboring insurgents, even when they are aware that there is just as much chance of killing civilians rather than terrorists.
I mean, I understand that in guerilla warfare, the death of innocents is often inevitable, as in that scenario it's "kill or be killed" or "kill an innocent rather than free a murderer".
But in any other scenario I don't understand how people can bring themselves to commit atrocities despite their conscience.
Answers & Comments
Verified answer
Militarizes don't.
People do.
Also, look up Stanley Milgram.
It will answer a few of your questions.
Everyone should be familiar with this work.
The foremost rule of soldiers is to obey the chain of command, this is always imprinted into soldiers since they begin training. Lack of strict command is like ordering a mud puddle, the army won't be an efficient, singular force.
And as you say, in wars it's either kill or be killed, there's little time for rational debate, primitive survival instincts and adrenaline kick in, only after battles do the participants realise what they have done.
But again, soldiers are trained to fight, if every soldier considers whether or not to take a life every time they fire a bullet, that's not much of an army.
HOWEVER, war-time psychology is very complex and varied, there's no one definitive answer for all wars and battles.
German balloons and later, the Blitz in WWII were designed to cripple British infrastructure, halt British military manufacturing and strike fear into citizens, as well as doing as much damage as possible by aiming at urban areas, such as Manchester or London, before a planned land invasion.
Japanese killing of Chinese civilians, as well as indiscriminate killing in other occupied Asian countries, reflected the lack of morality in Japanese ideologies at the time - the Japanese public believed they were "destined" to rule Asia, and superior technology gave them that power. Japanese soldiers simply viewed the rest of Asia as inferior to them, and civilians mere "primitive animals", hence Japanese soldiers felt no remorse at murdering unarmed civilians, resulting in 25 million civilians killed in China alone.
Hence, how can you rationally evaluate an incident when you're in the middle of it? We all have had times when we're so angry, then later realised how trivial it all was, and how foolish it was to be angry.
This is not an excuse for war mentality, if anything this means we have to consciously suppress these primitive "instincts", or "urges", whatever you call it, it's that ability to do what is right, instead of what feels right at the time, that distinguishes civility and barbarianism.