The PVP Guild(s) are competing against each other. Character Alliance doesn't matter, any points earned rank your Guild verses Alliance faction.
Remove faction bases and turn them into different start points.
Turn the Emperor into a Guild reward; for them to claim all the Keeps and hold them for a duration before the Empire is announced.
Converge all the top 10 into one ranking system for end campaign bonus rewards.
Reverse the bonuses for flags be given to all same faction guilds, so there are some synergies for same faction but same time, you may be helping your enemy.
Talberds flag your representing Guild.
Something on these lines..