Maybe you can refresh my memory? The ark in raiders was a macguffin. The only overtly religious character I remember was the imam. If you mean temple of doom with the Kali cult, that's closer except for one important detail. Other movies are careful to mentally distance depictions by having cults be underground or otherwise abnormal and isolated. Think midsommar, wicker man, etc.

The narrative of apocalypto is literally the mainstream Maya priests kidnapping and torturing people to sacrifice them before the protagonist is saved by the distraction of Spaniards arriving. I would consider the same thing with Christianity swapped a bit distasteful as well, but I can't think of any movies like that. Handmaid's tale would count, but that's a deliberate critique rather than unintentional stereotyping.