Ragnarok Online had a fun event for Guilds only called the War of Emperium. Basicly, there were a cluster of forts and once a week for a few hours the gates would open and other guilds could try to fight their way through and capture the fort. The guild that held the fort could defend it and spend money to purchase guardian monsters to assist in the defence. The guild that held the fort was rewarded with loot on a daily basis.

Adding someting like this could open up a lot of content for the game. You would have FC vs FC PVP on a weekly basis. You could have a variety of recipes added for crafters to make automations and traps for defense. The rewards could be additional company actions, unique housing items, even temporary buffs for other PVE content that gets stronger the more people from the same FC are in the party.