"I had planned on having one mage in a Raiding Guild and one mage in a PVP guild so i could get the benefits or each."

If they have removed the non-cosmetic stuff (I'm not sure that they have; they just didn't mention it), I'm going to guess that this would be the exact reason. Players will take any advantage they can get, no matter how minor and no matter how miserable it might make them, and there would eventually be people upset that they want to be in a guild with their friends, but they have to join a PvP-specced guild to get the benefits, or have their characters in different guilds for their different roles, or leave a guild they liked because they started doing PvE more often than PvP, ect. That would negate a large part of the design philosophy they've been moving toward more and more, which seems engineered to make sure that you don't feel like you have to do things you hate or spend less time playing with people whose company you choose for reasons other than "I have to spend 3 nights a week raiding with them" just to stay competitive.