To fix this, I've changed a couple of things. By and large I think it makes for a simply better RPG--I certainly haven't had any complaints from my eclectic mix of Christian and non-Christian gamers. Anyway, here are my changes:
Good and Evil
To reflect the variety of ethical stances in the world--including good folk still going down the wrong path, or folk following the right path and still being evil, I've seperated "good" and "Good." In order to be considered "good" for spells effects--like Holy Smite or Detect Good--you need to follow a good religion and be of good alingment. Conversely, if you follow an evil religion, you need to be of evil alingment to be consdiered "evil."
When a PC is created in my game, they need to select from one of four contradictory religions. One, "the Light of Heaven", is a fantasized version of Chrisitianity, with Judaism and Islam sprinkled in here and there. Another, "The darkness", is a declaration that there is no morality--evil, in a form that would be recognizable by a Levey Satanist by one of their own. The third, "Faith of the World", is the more familiar assortment of pagan gods.
Hmm... well, that's not nearly as in-depth nor as hard as I thought it was going to be. There are a bunch of other changes I've made which assume this start, which is why I probably thought the darn thing would take longer to explain. Ah, well.