Last I checked, not worshipping false idols was literally one of the 10 commandments.

Thus, Heavensward would be pro-Christian (If it was actually based off of Christianity, as opposed to a fantasy setting where there are 12 "Gods" that people worship)

Shadowbringers seems to be working somewhat on the idea of fanaticism and blind faith being not particularly good ways to live.

Also, you're skipping out on the fact that Stormblood was pro-religion. From the citizens of Gyr Abania worshipping Rhalgr (But being forbidden to do so because the bad guy Imperials dislike it), to the Kojin having their own religion where their gods inhabit pieces of garbage treasure. Even the Xaela's religion is shown in a positive light, as it gives tribes which would otherwise wipe each other out, some semblance of common ground.

P.S. Christianity isn't even a particularly popular religion in Japan so it's unlikely that it would be directly targeted by the Japanese developers (About 1% of the population are Christians... It's likely they don't even know much about Christianity as a whole in the nation with Shintoism and Buddhism being by far the more common religions in Japan)