Lots of people think the moon landing is some sort of conspiracy, despite the evidence, and I'm sure there's lots of stories about it (Transformers 3 springs to mind). But what about religion? I'm not trying to sell any point here, and I'm a Christian, but we believe without any hard evidence (I know, the Bible, but there's pictures (allegedly) taken from the moon and there's STILL a conspiracy). I wonder... could it be a story? Could you actually write the character Jesus? Or is this all ridiculously ridiculous? And in general, how far can you expect to go on things like this?
It depends on how compelling your writing is. And if it is being presented as nonfiction, how gullible your market is.
On the subject of religion, I don't think good writing has anything to do with it. People are biased, especially on touchy issues. You can't please everyone, and people are so finicky about religion, anyone, no matter how great a writer, would fail from the very beginning simply because he said something different from what the holy books say. That said, you can by all means write it, and it could be great. If it's controversial, people may even buy it in droves. But I doubt that many people would like it, simply because it would almost certainly conflict with their vision of what Jesus or God is.
There are multiple conspiracy theories surrounding most major religions. Pick one and enjoy the ride.
^ This. Also, in addition to making sure the writing itself is good, make sure there aren't any gaping plot holes left wide open, as that will undermine your story's credibility.
