I'm not sure it has been mentioned before, but I thought I'd throw an idea out:
One of the most common arguments against doing one thing or another in the cleric guild (murdering or stealing, mostly) is that one god or another would condone it.
So, I would ask: why not have certain guild leaders prefer (or disapprove of) the favored actions of certain gods? You would continue to train the kids--they are clerics, after all--but you would disallow whatever it is you don't want to be there.
And it would be a nice start towards creating a more pointed religion system.
-- Holy Scholar Diarik Erasto, Arcane Researcher, in search of spiritweaving.
http://www.livejournal.com/users/pensive-spirit/