I knocked out the two guys who were about to attack Auntie Ethel rather than kill them, and after the battle was over, she reacted like I murdered them.
I get how writing and programming a "pacifist" option for every encounter in addition to the typical one where you just kill whoever stands in your way would be a Herculean undertaking. I get that. But if for even the story-based encounters where only knocking out the enemies is a reasonable choice, such as in the case of two guys who are only attacking a woman because they think she kidnapped their friend, the game REALLY SHOULD recognize that the player hadn't killed them.
So if knocking dudes unconscious will wind up having no meaningful effect on the game at all, don't even include it. Just remove the option to deal nonlethal damage. Almost no RPGs even have such a thing as an option anyway, and it's extremely frustrating to have it as an option but for it to be narratively no different from killing.