You'll see the same happen whenever someone is critical of some deity or brand (say, Steve Jobs or Apple). This is a generic problem, and it is a hard one to solve.
I've always been a fan of analyzing all of the flags retro-actively to see if they were just or not and to have a per-subject matrix that would weigh flags from particular users. So anybody that is on the gravy train at apple would find their apple flagging permissions removed, and all YC combinator founders would have their ability to flag YC related threads removed. But that is a lot of work to implement and keep accurate.