I've joined factions a few time when offered by Maid Force, School of Magic, but all that happens is that I get a faction quest that doesn't seem to lead anywhere. Is there more that can be done with that?
I don't think there's anything special about it, but I think there's an advantage to joining because you won't receive solicitations from other factions.
The faction quests you get after joining are only for quitting that faction. Since you can join just one faction per save file, they basically just let you regret and switch—convenience feature, really.