The core principle of the game is: No matter who you kill, the quest should still work. At least the main quest, side quests not so sure.
Only the main quest (and possibly the origin quests) are going to be guaranteed to work. If Bob gives you a quest to find 15 Bear Arses, and after you take it, instead you kill him and set fire to his shop, you're going to fail that quest, as you should.
