Ol' Willy
Arcane
Almost. I did it a way back; technically you don't have to kill anyone, but robots near ZAX, rat king and ranger in San-Bramin were to be removed.Regarding the combat skills - all of the main quests are designed in a way so you can avoid the unneccessary bloodshed. I didn't try to be pacifist but something tells me that Sonora can be reliably beaten without killing anyone.
Ranger should have a speech option: either a bug or oversight.
Rat king could be killed by dynamite or environmental traps.
But those fucking robots in the bunker... stealth doesn't help, only if you run past and soak damage.