Despite the fact that humans possess the capacities of sympathy and empathy and the resultant compassion there have been and continue to be atrocities committed by humans on humans.
How do these humans continue to function knowing what they are doing to their fellow human being. The answer seems to be a disconnect. If you can reduce them to less than human you can commit the atrocity without the attendant feeling of sympathy. This was successfully done by the German Nazis during World War Two. The Jews became less than human in the minds of many Germans. The propaganda machine of Adolph Hitler was very successful in its goal of creating a monster against which to struggle.
There was many gulags where humans became more or less animals and were treated the same. Starvation and disease was rampant at such facilities. The final solution was ready at hand. The immensity of the moral crimes was greater than many wanted to or could imagine.
Who knows what great minds were burned up in Germany during these horrible times. I imagine many an atheist arose among the Jewish population as the prisoners realized… no god was coming to stop the nightmare.
The mentality that possessed the Germans to do these horrible deeds at the behest of a madman still exists today. All you have to do is look at the latest war machine racking up bodies. I imagine that possessing the will to pull the trigger on another human being could be necessary at times. I think though, that those that have had to do it are permanently irreparably damaged by the need. How can you turn off such an ability to disregard the empathy which tugs at your conscience and not be messed up. How could such a person ever be allowed back into civilized society? How much therapy, if there is appropriate therapy in existence, would someone need? How would you ever know that a person has been rendered normal and trustworthy once more?
I grant that a pacifist would not long last in this world. Isn’t that the problem, after all?