Do you have an example save?
Afraid not since I use some tweaks adding new units to the roster among other things so it breaks savegame compatibility. Kind of invalidates my claim but I doubt I touched anything having to do with religion spread.
An example which may work, loading the 600AD scenario as Nubia, using WB to change to no state religion, remove religions and temples from a city, adding a Pesedjet temple and a Jewish missionary, it can spread the religion and that removes the pagan temple.
Same with Justinian, granting open borders and using a missionary in one of his cities it does the same thing, rather than letting the temple stay like I thought I saw with Greece. But what I'm seeing now is that the pagan temple is removed but it can still be built again if there's just Judaism in the city. After spreading Orthodoxy the option to build the pagan temple is gone.
While at it, I'm also noticing the still pagan civs (Mali, turks, Toltecs...) have the Statue of Zeus available for construction. Guess it's missing from Scenario.py. I'd also propose these owner changes if you're interested:
iAlKhazneh : (iEgypt, 100), #not sure but it kinda fits?
iSalsalBuddha : (iKushans, 570),
iJewishShrine : (iEgypt, -957), #because Moses... well maybe not
iShwedagonPaya : (iBurma, 1362),
...
iSaintSophia : (iRus, 1031),
...
iMachuPicchu : (iInca, 1450),