These people don't even read their own literature. The Catholic church's ban on alchemy is about falsely claiming something is a valuable metal in order to pay for debts. It has nothing to do with the occult -- the ban was because it's a sin to lie / cheat / steal. A saint is even on record saying that alchemical gold is ok if the end if product is real gold.
With that context, of course God doesn't give a shit if you use SQLAlchemy as long as you aren't using it to defraud people. If you were defrauding people, it wouldn't matter what tool you used.
I mean, these are the same people who won't watch Big Bang Theory because the title is heretical, or believe that playing Magic the Gathering or Pokemon TCG are literally summoning demons and spirits into the world, or who believe that playing D&D is doing the same. Rationality is not exactly their strong suit.