I dunno, only joining one guild would mean leaving out three thirds of the guild content on a single playthrough.
Maybe the Mages are at odds with the thieves, the warriors with the Dark Brotherhood, making it possible to only complete two guilds per playthrough.
I suspect every guild will be joinable on one play through simply for the mass appeal of it. Lots of folks would be pissed they couldn't join a guild. Plus, the reputation system is said to only hold within each city so that would seem to imply guilds in different cities won't take into accounts the actions of a player in another city.
Of course, I don't know, just my speculation.