I think the cleric issue in general becomes easier to deal with if you have clerics draw power from divinity itself, with gods/domains providing some spice on top of that. In a way, the cleric class becomes the ice cream, and the domains become various toppings that add flavor to the underlying stuff without fundamentally altering its nature.
I also like the 4e concept that divine casters get a one-time infusion of power that allows them to access the powers of divinity, and once that is done it's permanent – somewhat similar to how Slayers (as in Buffy the Vampire Slayer) work. So should a cleric go renegade and/or apostate, the solution is not for the god to take their powers away. They can't do that, any more than the Powers That Be can de-Slayerify Faith when she goes renegade. The solution is to deal with the apostate.