So you want a game that you'd expect to be violent...but has at least a permanently viable non-violence option. A lot of games have the option to kill someone or knock them out for roughly the same effect. MGS4, DE:HR, those sorts of things. As far as games with diplomatic or completely non-confrontational options...maybe Dishonored? Mark of the Ninja? Mirror's Edge sort of discourages gun combat by making it impractical more often than not. Often they don't really bother with a non-confrontational system alongside when the game is 99% of the time going to be played in violent lethal or violent non-lethal ways.
EDIT: And since I've read a few other posts, I think I need to state that I love violent games and most of the time, games like fantasy RPGs and MMOs and that sort of thing would be boring as hell without violence. There are actually plenty of non-violent games that have no violent option, including entire genres, and I'm happy for it to stay that way. In a world like Lordran, Skyrim or Hyrule, violence SHOULD and WOULD be the best option in many scenarios. If you get jumped by bandits, what are you going to do? Convince them to let you go, when you're clearly decked out in the best armour and weapons around and have gold spilling from your pockets? You're going to cleave those bastards in half. What if the enemies are all mindless servants of your evil nemesis who are only trying to kill you, or simply insane zombies who have no other impulse? I think there is a lot of opportunity for games to have diplomatic or non-violent routes, and it could be done more often (doesn't have to be combat ALL the time), but it certainly isn't a bad thing.