In general, this is a good idea for religions. This would allow a "sect" flavor. For example, each member could choose the specific god they serve, and thus join that "path". The adherents of God A have a different focus than the adherents of God B, and could have secrets and plans that are not shared with the others.
Not sure that it really applies to guilds. There are no such things as "rebellions" in guilds. You cannot take over by force, or revolt and toss out the other people. Whoever has the highest ranked guy wins, period. You're all in a guild together because you share the common interest and factor that brings you together to form a guild. If that common interest and base isn't there, then you should probably be in a different guild.
Splitting it to allow religions to have it and guilds not would also allow for some separation between the two.
