[Coda]

Most RPGs rationalize it by setting the conflict in a place where violence is justified.

Self-defense and war are the two most common justifications -- either the enemies are violent invaders themselves, or the enemies are in the way of you bringing an end to the war. The enemies being uncontrollable/wild/insane/etc. is another common justification.

In almost all cases, the part that sets the heroes apart from the enemy is that the enemy is the one initiating hostilities and the first to display lethal force and intent. When the enemy hasn't initiated active hostilities, the enemy is still causing ruinous harm to the heroes and/or the world, and the heroes have no choice but to take action.

When these justifications AREN'T in place, it's usually to MAKE you feel like something's not right about the characters' motivations.

Sometimes it IS completely unjustified, but in those games there's generally not much of a plot at all -- a flimsy framing mechanism to give the action an excuse to happen, if anything.