Manipulating this common formula is what made the religions of the Thief series so compelling, even as they tapped into those stylized and well-trodden fantasy tropes of Law, Chaos and Neutrality made ubiquitous by Dungeons & Dragons and its relatives. Every faith in the world of Thief is dogmatic, scary, malevolent, villainous, and imbued with actual mystical power. They are cultural forces as well as spiritual forces, permeating the pores of the setting from mud to spire, and the games' protagonist works with and against every religion in the setting at one point or another. They were the many and varied establishments of the realm, and great establishments make for great outsiders.
These religions are flawed in their harsh zeal, but they also believably offer something that characters in the game conceivably want. It's a lot easier to think of the 8-bit figures roaming the game world in The Dark Project as people when the religions they subscribe to or resist have some logical appeal.
The Hammerites promise protection from a scary, dangerous world filled with crazy barbarians and cutthroat criminals; they offer electric lights in the dark. The Pagans promise a wild, hedonistic existence free of strict Hammerite tenets and full of honeyed wine; they're an escape from modern complexity to old simplicities.
That these ideologies are melodramatic abstractions is clear, but they still offer a nuance that a straight-up evil god doesn't. It easy to see how these groups might have started out all right and progressed into the antagonistic organizations you're up against.
For me, it was when I heard a particular line of dialog from a Hammerite on patrol that I realized they were fanatics, not lunatics. "If the foundation is weak, do you wail and gnash your teeth? Nay, you tear it down and you begin anew," says the Hammerite. There's a reasonable message in there about progress and perseverance, which helps make the Hammerite religion believable. Then he says this next line with some menace and I'm back in the game, remembering that he's wielding a huge hammer: "So shall it be with all of my children, whether they be stone... or flesh."
One of the keys to Thief's immersive world is character, and Religion is used to flesh out the game's characters. Thief also uses its fantasy religions to evoke the themes of freedom and disobedience that are essential to its gameplay. And it does so without tripping over its own commentary. Gods and fanatics should still be compelling characters, which means they should surprise us sometimes.
Commentary in games often comes in the form of monologues from NPCs. In Thief, it comes from seeing the religions in action as you prowl around their places at night; it comes from excerpts of fictional scripture offered enigmatically during mission briefings; it comes from the architecture. The game's castles, prisons, churches, and tombs are essays describing the game world and its themes.
The Dark Project's abandoned cathedral is a monologue on the Hammerite vision and capacity for a medieval steampunk world of stained glass and clanging magical machines... and how that vision leads them to such trouble that they'll board up a grand cathedral full of zombies and just walk away. It's about the old versus the new.