I suspect it's increasingly hard to be freshly creative in concocting a religious dystopia. Perhaps such fiction too easily falls into the smug-atheist trap to handle empathetically, as you suggest, a flawed utopia with the True Believers whose existence gives their society such integrity as it possesses.

I read Heinlein's early short novel "If This Goes On --" (1940) when I was quite young, and it was probably the first I ever read about religious dictatorship. Although it's fairly straightforward, I think Heinlein gives his believers some credit for believing what they do, and is not smug about their situation.