I think I similar unlock button as the game already has for appearances is the way to go. By default, the game only offers lore-following appearance colourations. With the click of the button you can play a human with green skin and red demonic eyes, if you so wish. Apply the same to domains. Have suggested domains in each god's description and only offer choices that makes sense for default. Have an "unlock deity-domain choices" check clearly displayed that allows the player who wants to to pick whatever they want. Sensible and respectful to the source content and allows maximum customisation.
A cleric worshiping A god of war shouldn't be getting life domain powers, for an arbitrary example.
I don't really think a "battlefield medic"-type cleric of Tempus who focuses on healing to return soldiers to the fray and thereby prolong/intensify wars is actually that bad of a concept, particularly since the Life domain's heavy armor proficiency already implies some emphasis on martial training, but I agree with your overall point that some combos don't make sense.
Yeah, not to mention war-adjacent deities like Tyr, Torm, or even Lathander. Not every god of War is fucking Garagos, there's no reason The Red Knight (Goddess of Strategy, ie Faerun Athena) wouldn't see healing as an important part of War.
