Just a factual note: the series' "Protestantism" and "Catholicism" have nothing to do with Christianity. For one thing, Catholics don't believe in predestination (by doctrine, anyway); some Protestant sects (e.g. Calvinists) do believe in it. And, obviously, once you start adding in a "goddess," you aren't talking about Christianity any more.
Rather, the author just used the terms, so they are:
1. portraying two opposing sects of a single religion
2. having one arise from the opposition to the other
3. using the meanings of the terms themselves (possibly) — Protestant=protest; Catholic=universal
Edit: a later chapter confirms no.3.