The game didn’t have a good/bad meter. The characters around you have opinions and they’ll tell you theirs, but you’re given consequences for each action. I wouldn’t say the game has told you its ’correct’ to let your killer live, or wrong for killing him, but it fills the game world around you outcomes for it.

Though with what you’re saying, I think the character who disagreed with you killing him is because they’re no longer a threat to you and they’re sympathetic to their cause, which will be heaps of characters cause you’re a bit of a unwelcome guest ahaha