Yes, I do allow clerics to follow non-deific philosophies and faiths. The way I usually do it in the Eberron game I run is that your access to spells depends on faith, not the gods, because faith is in itself a powerful force that influences magical energies. Thus, another level of divine spellcasting is an indication of the growth of your faith, which exhibits itself in the physical world. There is something about the white fire of belief, and I like the idea of adding an element of conviction, faith, belief to a game.
But what I wouldn't allow is a cleric who has no faith in anything whatsoever. It still bugs me that one of my friends insisted that my requiring a cleric to have faith was unfairly railroading the player from playing the character he really wants to play.