It's never been implied that you have complete freedom of speech on Smogon. Allowing moderators to use their own discretion in deciding whether or not a user has "crossed the line" when discussing these issues shouldn't come as a surprise to anyone. There's no one rule that can be made to prevent this, as "don't insult these X groups" is going to kill any discussion on them period. "Don't go too far in insulting X groups" is always going to be open to interpretation.
I believe that making it known that moderators will use their own judgement will at least deter the less rebellious from going too far, and anyone who still does it probably wasn't going to be a good user anyway!