Another thing I've considered is having specific types of flags on comments, and having them have different effects. E.g. there could be a flag for incivility, and if you got enough of those (maybe in proportion to your total number of comments) you'd actually get kicked off the site temporarily.
However, I don't see an algorithmic way to use flagging in such a situation. The new control mechanism would be subject to the same problems that led to the comment being upvoted in the first place.
I'd like to see the mods experiment with a more authoritarian approach. When a comment sucks, I want the mods to impose their will upon the populace, informing everyone that the comment sucks, regardless of its upvotes. Flags could play a role.