I can't remember if you kill people (deliberately) in Monkey Island..
But if not that, then probably From Dust and/or the various Phoenix Wright games, except you're usually solving murders, so that kinda throws it out.. but it's not your typical blood-splattery, body-counting kill-fest, so maybe it does count.
Oh! Recettear counts! I don't think skeletons and slimes count as people, and the majority of the game's storyline doesn't even take place in a dungeon.
Otherwise there's always the Portal games (replayed 1 after finishing 2), EVO (which only involves eating animals, unless you count those bird people in the one area, but I didn't play it that far this time).
Kinda sad when you think about it. Everything from Mario to Skyrim involves killing people, especially when you take into account the RPGs where the Goomba's and Koopa's really do talk and have personalities.
EDIT: Oh yeah! I played Pokemon Yellow a few months ago. :3