So just allow you to kill them all but still have them in the game, you mean completely rewrite it so its a series of quests? Just allowing you to kill them just takes away content, again some of us like story (which the game already leaves a lot to be desired). Without spoilers, just killing them makes two largish places pointless accept to look at.
Then have a questline for destroying the thieve's guild that makes those places worthwhile in other ways. Like, maybe you set up some kind of good-guy-brigade neighbourhood watch thing in those areas. The idea here is to have a counter-quest tree that's *just as interasting* as the thieve's guild quest tree, so that you can choose one or the other and not feel cheated either way (and you can't see both in one playthrough, which is also good IMO).
-Robin