I liked the ending. Lots of very good SF has used religion as a springboard for stories (e.g., James Blish, Gene Wolfe, Cliff Simak, Michael O’Brien, Cordwainer Smith, C.S. Lewis, Walker Percy, Anthony Boucher, Richard Matheson, R.A. Lafferty, Michael Bishop, Ted Chiang, Phillip K. Dick, Michael Flynn, Tim Powers, Walter Miller, etc.) It’s a huge part of the human experience, why shouldn’t it be used?)
Most SF involves supernatural or fantastic elements and tropes which include things that our modern understanding of science doesn’t recognize as likely, anyway - ESP, time travel, FTL drives, psionic powers, “quantum leaping” etc. - why quibble at religious elements? As is often said, what most people think of as SF is really just fantasy. There are probably only a handful of real “science” fiction stories out there, where plausible science and the scientific method are plot elements - “The Andromeda Strain” and “The Martian” come to mind.
On Quantum Leap, it was previously recognized that Al, an MIT-trained scientist, was religious and believes in both God and the Devil, and was also a little spooked by things like the Bermuda Triangle. When Sam jumped into a priest’s body and was dying, Al broke a long-standing enmity he felt towards the Church and prayed for Sam, which was portrayed as probably efficacious.
Series creator Donald Bellisario is Catholic, if memory serves (like Al), so religious themes weren’t uncommon on the series.,