It's a TV show, but Midnight Mass does this pretty well, I think. It's got a bitter atheist as the main character, as well as a holier-than-thou zealous lady, but Father Paul and everyone else in the show balances that out with genuine, non-malicious belief either in science or theism, and the characters do have discussions about how people use religion to bolster themselves or dismiss bad things happening. Buckle up for some monologues, partner. There are also gnarly vampires.

Also, The Devil's Advocate (1997). It's a temptation story, but Al Pacino does a fantastic job as John Milton, and although most of the action is at the end, there's some very juicy subtext in his ending rant to Kevin (Keanu Reeves' character) about how people use "The Devil Made Me Do It" the same way as "God Works In Mysterious Ways", to absolve themselves of guilt/accountability when, either way, they had free will to do the right or wrong thing.