Perhaps 'approved guilds' may earn some special part in the settings themselves, such as being in a book in the library. If the guild dies, have it be, as suggested before, 'history' If the guild's ideas changed, have it written, "In recent times however, the guilds ideals have changed" blah blah blah. But If a guild is within settings parameters, and seems to be a fairly open guild (not secret or intended to be unpopular) or is an infamous guild (Thieves Guild anyone?) then perhaps some literature should include it. This might also help that guild with recruitment in a roleplayed way, for if there is books in the library, people may read about these guilds and wish to join them. Thenagain, that goes back to favoritism, but like Raken said, if it isn't, then there is no worries. The Developers are not playing favorites, they don't take their job lightly, so as long as they know they're not then we're fine. I'm fairly certain Xillix at least would not allow anyone to do something for a guild out of favoritism.
As a note, this would ALSO put these guilds under a certain scrutiny of the settings team and thus they'd have to watch where their history leads them and such.