If you have to ban DLC because some get it before others, then Arcade Edition should have been banned because it was available in only a select few arcades, giving some an unfair advantage.
You can take this argument too far and argue that console exclusive characters shouldn't be banned of course, but given that console exclusive characters are for non-console owners the price of the console plus the correct copy of the game, I think it's reasonable to ban them.
In fact, you could make a very compelling argument that certain DLC exclusive characters should be legal in tournament, but only if the price of the console + game isn't that much so you can reasonably expect most of your scene to own that copy. If 99% of the MK9 scene owned the PS3 version, Kratos might well have a case for being legal.