At any rate, I'm a huge Morrowind fanboy, and if I recall correctly, doing the main quest "properly" requires you to only kill Dagoth Gares, the leaders of Redoran/Telvanni/Erabeninsum, the Urshilaku ancestral ghost, and of course Dagoth Ur.
You don't need to kill the leaders, since you can bypass the entire Nerevarine/Hortator series of quests by having high enough reputation. I don't remember if you need to kill the ghost. Dagoth Gares is definitely the first guy you NEED to kill to progress with the MQ.
There are two alternate paths that allow you to bring that down to just Dagoth Ur.
Depends. The "back door" one also requires you to kill Vivec. The "cheese the fuck out of alchemy" path is I think the only one that only requires you to kill Dagoth Ur.
Technically you're not "killing" Dagoth Ur in combat anyway though.
I'm pretty sure the faction quests, with the exception of Morag Tong for obvious reasons, have a similar ratio of non-violent quests to mandatory violence ones.
Depends on the factions. Fighters Guild have a lot of kill quests because, you know, Fighters Guild. Thieves Guild have a few towards the end, otherwise they're very much a nonviolent path (and some of the kill quests could done without the killing if you'd done other quests first). Temple IIRC had no kill quests.