Since the capacity for guild members can't go any higher, and there are some guilds that wish to work with each other... (IG:Eyoo + NegaEyoo) Why not a guild alliance system where 2-3 (two to three) guilds could become one, BUT there's a choice to either keep one guild name or keep both/all of them, and add "ALLIANCE" next to their merit title in the info menu. An optional method to show that a guild may be in an alliance is to add a small blue gem next to the character's name in game and their Guild name in lobbies as shown below. The way it works is, the guilds continue to have their separate Ladder Points so they don't stack. A new Alliance chat tab that consists of the alliance guilds is made for communication. If the guilds are in an Alliance, they cannot verse each other in the Guild War channel, but they can team up and verse others that are not within the alliance~
Support 100% If I also may add: Guilds that have an alliance should be able to team up and face other guilds. The teams would earn their own individual ladder points and increase/decrease their own rank and not affect the guild they team with. Example: DarknessGang vs NegaEyoo & Eyoo DG can use 4 members. The other two can use two members each or 1 and 3. I havent really looked into pros and cons about this, this is just expanding your idea into another direction.