NOTE: I'm including spoilers in here, but I'm assuming if you're going to try this you're familiar with the game already.
Hm. Two of the main quests specifically require killing, so that would be a problem for you right there... unless you're willing to exclude House Dagoth members from your pacifism, of course. You'd have to skip the Hortator and Nerevarine quests (Redoran and Telvanni, as well as the Erabenimsun, require killing regular NPCs) by having a high level and reputation.
I believe you can technically do the Imperial Cult without killing anyone. I'm not sure about the Thieves' Guild, but that's probably doable as well. Both require you to know what you're doing, of course. I'm fairly sure all of the Great Houses absolutely require killing people to reach the top rank, though. Hlaalu's the best in that regard, I believe, and may be possible, so long as you don't mind having to stop at the second part of your stronghold.