Guilds don't need to be completely politically aligned. You can keep your A/H faction but let people group together.
Heck, outside of very few raids like BoD and encounters like Gunship or the pvp encounter in ToC you don't even fight each other. Lorewise it makes less sense for A/H to kill each other than to work together since this is not the same Horde in WC1 and 2, but heck gotta give people their REEEEEEEEEEEEEEEEEEEEEEEEEEEEEE PVP reasons, heh.