The larger problem is that Faith is one of the base yields baked into the game's systems, and from/to which so many other elements of the game work. Pantheons, Religions, Holy Sites and their faith-buildings, "religious" city states as well as the military city-state that allows faith-purchasing of city-center buildings, as well as other interlocking parts of the game. Without the Faith Yield systems, Great Prophets, Missionaries, Apostles, etc., would be useless and unavailable which might or might not cause the game to CTD at points wherever an ai tried to do anything faith-related.
If you wanted to get rid of the effects of Pantheons (but players would still select Pantheons altho they would have no effect) you could remove all the modifiers for Pantheons in table <BeliefModifiers> in file
Code:
C:\Program Files (x86)\Steam\steamapps\common\Sid Meier's Civilization VI\Base\Assets\Gameplay\Data/Beliefs.xml
But then you would also have to check that the code within the expansions don't add more Pantheons or adjust the effects of any Pantheons within the files of the two expansions. Whether this would caused the game to CTD or otherwise wig out from there not being any actual effect for selecting a Pantheon is something you would have to find out the hard way.