Nation is the story of two children: Ermintrude may just be the Queen of England now that a plague has struck down most of the royal family. Mau is the last survivor of the Nation, a tribal people living on a south-seas island that has been destroyed by a tsunami. They are both lost and adrift in the wake of terrible tragedy, flung together on the island of Nation. They both are blessed with doubt about the theologies of their ancestors — and denied its succour. Together, they discover science, and use it to weld together their people and save them from despair and evil external forces.
I’ve never got into the Discworld novels, but his Johnny Maxwell series is still a favourite. He’s also firmly on the side of rationality, and it sounds like the above may have something to say in that regard. I’ll keep an eye out.