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.