I thought this synopsis contained a nugget of unintended irony. Why would it be difficult to include it in your SF or fantasy world without making it a caricature? Could it have to do with absurdity of most religious beliefs? Unless your religion is so vague that it limits itself to a largely indifferent, hands-off Creator, it can be characterized by Heinlein's famous quote: "one man's theology is another man's belly laugh". Ironically, your readers might think that a supernatural being you created is ridiculous, but the one they believe in is not, though they differ only in details.
Mikal Trimm, Matt Cardin, and Matthew Bey on Religion in Worldbuilding panel.
Somebody in the audience held Frank Herbert's "Dune" as an example of a SF novel in which religion is done very well. Fair enough -- I don't remember it being ridiculous. Somebody else mentioned an Arthur C. Clarke's story that incorporates religion very well. In that story, missionaries go to a distant corner of the galaxy to preach their religion, and reach a star system where all life went extinct thousands of years ago when the star went supernova. Turns out, that was the Star of Bethlehem. I think the story makes a good point, but it avoids making a religion look like a caricature at the cost of making it look ironic, arbitrary and cruel -- just like in real life. So that was probably not the point the panelists were trying to make.
I was disappointed how one or two people in the audience perpetuated the myth that the "New Atheists" are just as fundamentalist as religious fundamentalists. But it wasn't the right place to get into that debate. However, I had a chance to pitch my Science and Religion in Fiction book club to the audience (well, it's not mine, it's part of Center For Inquiry, but I'm the organizer), and I got a few people interested. Whether any of them will ever make an appearance at our meetings, is anybody's guess. (Mine is "no". :-))
More on the similar topic: my blog post on Creating a Believable Religious Society: an ArmadilloCon 2004 panel at ArmadilloCon 2004.
Pictures from Armadillocon 2010 are in my photo gallery.