Remember Me's protagonist Nilin doesn't go out of her way to kill people. She just beats them up, and alters their memories so they don't wanna fight anymore. Infact it was a goal of the developer to make a less kill-fest sort of game.
I'd say Batman, and Catwoman aren't in the business of killing either, so the Arkham Asylum/City games might be up your alley.
The Way of the Samurai series allows you to beat people up bare handed, or with the blunt side of your weapon(s) so you don't kill a person. Infact in WotS 3 it's encouraged that you knock people out as every person you knock out as opposed to kill, you unlock their appearance for your character as a customization option!
I doubt it matters a whole lot, but Dynasty Warriors series doesn't have a "kill" counter, it has a KO counter. Despite being one of china's most battle ridden eras, a surprising amount of the enemy officers you fight survive the encounter to fight again later.
In Dynasty Warriors 7 Empires, and in several other Empires installments (They're a mix between stand-alones, and expansions as often there's carry over, but you can just buy the often cheaper empires game, and play it without the main game), when you capture an officer as a ruler, you have the option to recruit, release, or kill. You can even turn off officer deaths, and remove the execute option.
There's been pacifist runs in the fallout series, though I've never really tried those.
I could prolly name more if I put my mind to it, but there's a short list.
Kinda reminds me of a part of Sun Tzu's Art of war that I can only paraphrase atm.
To kill one is murder, and makes the killer a criminal, and is punished.
To kill many makes one a greater criminal.
On the other hand the people you kill in games are generally bad people. They take up arms against you to prevent you from saving something, or someone the enemy is putting in peril. The people you kill want you dead. You're often faced with no recourse but to fight.