It sounds like he came to believe that American activities in Afghanistan were causing more deaths of innocent Afghans--like when the child was run over by the tank. Something along the lines of "Thou Shalt Not Kill" (at least unless there is a greater good) probably weighed heavily on his mind.
What this soldier did was wrong and irresponsible-- his disconnect from the real world made him not foresee that his choice would endanger others. (Not to mention himself--did he really believe it would be all flowers and chocolates when he ran into some Afghans and Taliban??)
However, I will defend a person's right--obligation, actually--to consult their own conscience even in the most difficult times. That's why we all read the dystopia books like 1984, Animal Farm, The Giver, etc. - to remind us that it's not okay to just "go along" with higher authorities! Remember the psych experiments (done at Stanford, I believe) where ordinary people were willing to administer extreme electric shocks to "patients" because a man in a white doctor coat was telling them to do so.
I think this kid was stupid, naïve, idealistic, living in a fantasy/adventure world, and his upbringing left something to be desired. I do not believe he is evil.
Of course seeing a child being hit by a vehicle is a terrible thing to see - no matter where it happens it is a tragedy. How many children were hit by vehicles in the U.S. while he was away? Is there some allegation that what he saw was done purposely, or was it just an unfortunate accident? How many children have been strapped with explosives by the Taliban and used as human bombs?
I agree with you that people should follow their conscience if they think something is truly wrong or they are asked to do something that is wrong, but it's not sounding like that was the case here. He was just asked to stand at his post.