[Death by Mirrors]

Are you aiming for a scary, dystopic mood or more like thrilling adventure with a happy ending?

Because if it's the first, make religion and government the same entity, but in a way the reader constantly is challenged in their assumptions (eg. a completely peaceful world can't see any actual progress, mankind needs a certain level of struggle to evolve their technologies and knowledge; so maybe the cult taking over means a change for the better, but then again there is something fishy about the way they handle some things... keep 'em in a constant grey area where it's ultimately impossible to choose sides)

If the latter, religion and government being seperate from each other makes one of them easier to overthrow if the other turns out to be an unexpected ally for the fight.