At this point (especially with warmode) I think the only solution they have is to allow horde and alliance to group.
If they push alliance racials or bonuses too far then everyone swaps, if they don't nobody will. The only real solution once it's this far gone is just let them all run together.
Make guilds "neutral" and keep races restricted to their faction hub(s), but they can run a raid or dungeon with anyone. Wouldn't be surprised it they even push it lore-wise near the end of the expansion.