What you describe (religious people giving bad ratings) is a fundamental problem with one dimensional systems. They just won't work as general purpose reputations which are certainly multi-dimensional.

An ebay seller rating can be one number because it pretty much just means "Does this person send what they posted".

But a general reputation covers so many things. The solution is probably a bunch of different ratings, maybe connected or maybe not.

The ultimate answer probably looks a lot like no answer at all, people just making connections and vouching for each other to make new connections. Tools for finding paths of trust of arbitrary types types would be nice. I have a great reputation without being involved in any official reputation systems at all.