Just because you clear an area before you're sent there on a quest shouldn't break the quest. Am I not supposed to go to an area before I'm sent there?
Er this is TES, thats precisely what should happen. Not to be an a-hole here but thats what TES is about in some respects, a big sandbox you can mess with and if your not careful, screw it up. Morrowind had I think hundreds of quests that were extremely easy to break if you or someone else killed a required NPC. Thats part of the game, a design decision if you will. There are some characters that cannot be killed in Skyrim yes, but most of these are for the main quest or are a no-no to kill (children) there are plenty that can be killed though which will have an effect on your game in some form or another.
So it really means you need to learn self control. Just because you can kill someone or something does not mean you should do so willy nilly.
Thats TES for you, love it and hate it.