Let me put it like this: why do you think people don't ban certain moves on certain characters in fighting games? The moves are part of the fighter and essentially make the fighter what it is. As far as a competitive level is concerned, Pokemon are nothing more than stats and numbers on a screen. Altering those stats and numbers changes the Pokemon itself and that's completely outside of our jurisdiction. We're playing competitive Pokemon, not "Smogon's version of Pokemon".
For example, we have Phione, the completely watered down version of Manaphy that's not even viable in standard UU play. It's about exactly the same, minus the moves or stats that made Manaphy broken...oh wait, that's exactly what Manaphy is.
Some may say, "Well, we can just draw the line at moves, right?"
Nope. We already have a standard set for ourselves here at Smogon, which is to remain faithful to the game mechanics. This ensures that we're still playing competitive Pokemon rather than our own game, and sets a reasonable line for us not to cross in the policies we implement. This is the main threshold that shouldn't be crossed.
Basically, if we ban ANY aspect of a Pokemon inherent to the Pokemon itself, we are no longer playing competitive Pokemon, we're just changing the game. We should not be able to do that because it goes against the very essence of competitive Pokemon, which is the Pokemon themselves. I believe that crossing this threshold compromises the integrity of the game we play, and leads to an entirely different product, invalidating all the time and effort we've spent over the years to ensure that this would not happen.
Writing general rules that apply to all aspects of competitive play (like evasion clause, OHKO clause, banning certain Pokemon from standard) is quite alright as far as I'm concerned, but getting specific is crossing the line, and is more of an indicator that the Pokemon itself should be banned rather than the move.