The GvG games I've played they've matched by either points or member strength w rewards based on beating that guild only. Stronger guilds will have it easy at first but will eventually be paired to someone near their abilities.
If guilds either get to choose matchmaking or if rewards are based on a type of global rank, it's going to be a complete and utter mess. Guilds will break up, people will get kicked and weaker guilds will just be punching bags for spenders.
It has the potential to add a fun element to the game for all to enjoy or be worse than tournaments.