My character joined them, and is now a ways along the questline. I'm curious if a more well-behaved character can help clear Riften of its troubles instead of adding to them.

I've always wondered that myself in Bethesda games. I'm guessing you can physically kill off everyone in the guild, but I doubt that it will have any effect in the story. I always wished they would- some kind of reaction in the game world, even if small, would be nice. It's an rpg, so someone playing a lawful character would definitely find wiping out a diametrically opposed faction desirable. With the way your decisions affect Skyrim, you'd think it wouldn't be too difficult to have the game support a move like that. It wouldn't even have to be a major quest- just something that kicks in after it's done. Maybe something that could open up new quests?

I guess the biggest 'problem' with this is that any lore they'll add on skyrim in the next game, might not match your actions. If they make the game too free they don't have any room left for lore