War is brutal, ugly, soul destroying work. It is done by killing the enemy, his infrastructure and terror. Sadly terror does work and will remain a tenet in war forever.
In the words of another Freeper, "If you are not willing to kill your enemy and all that stand with him, surrender for he has already defeated you." Without the civilian population a military can not function. They are part of the military machine.
Just to pick a nit, Kokura was the next target, but cloud cover meant that Nagasaki was hit instead. Kyoto was on a target list, but Sec’y of War Stimson asked for it to be removed because of its cultural significance.