A short list of fantasy / science fiction / speculative fiction where faith is a major element.

Bowker, Richard – Forbidden Sanctuary
Cogswell, Theodore – Spock, Messiah!
Del Rey, Lester – The Eleventh Commandment
Easton, M. Coleman – Iskiir
Elgin, Suzette Haden – Star Anchored, Star Angered
Farmer, Philip Jose – The Stone God Awakens
Foster, Alan Dean – Cyber Way
Grabien, Deborah – Plainsong
Kemelman, Harry – Friday the Rabbi Slept Late
L’Engle, Madeleine – The Wrinkle in Time series