I think PVP has to be completely separated from PVE. Completely.
Different databases, different spells, buy cheap wow accounts even a different launcher. If the person wants to do BGs or Arenas, he logs out, enter another .EXE executable, and then gets sent to an isolated area from where he can't leave. May be a Sanctuary, with vendors, AH, trainers, reforgers, banks. And from there he queues to BGS and Arenas, or duels, including against people from other faction.
What about World PVP? In there, applies the rules from the PVE database... World PVP is not balanced anyway, you just bring new players to counter the attack.
Only then I think PVP can stand a chance to be almost balanced.
PVP gear already makes players choose between those two games at the moment. Yes, you can acquire both, but you could play both under that system too.
You'd keep the chat so it worked across-.exes, obviously. Chat aside, what problems does it create?
To start with it's a barrier to entry for casual players. Forcing people to shut down their current running game, and making them log into a different client would prevent a lot of folks from bothering to PVP in the first place.
Then you have a secondary issue of the fact that Blizz would need to allocate additional resources to maintain separate PVP and PVE clients, for all platforms, in both 32 and 64 bit setups.
I'm also failing to see what actual benefit it would provide anyone; fast wow gold PVP and PVE seem to co-exist fine for me as-is.