PVP does effect PVE in terms of balancing classes, but I think that's fine. If classes need balanced they need balanced. But it's complicated to do so because you need to balance a class and at the same time balance any PVE battles that might be affected by it.
Personally I think they should section off certain abilities to be PVP exclusive and other abilities to be PVP exclusive. E.g. Say there's a global ability everyone can have that removes all binds/sleep effects (like everyone has sprint) but with a 5 minute cooldown and only available in PVP. Then something like Paladin's Hollowed Ground could be PVE Only.
And we should have a separate armory for PVP gear, and the Action bar's should be independent between PVP and PVE sets. E.g. if I go to PVE gear I get my PVE hot bar setup, but PVP gear and I get my PVP Hotbar setup.