Ngl, I start to get rather bored when it's "Church that's totally not Religion 'C' is totally Evil" something that made like Faraway Paladin, and some other feels like a breeze.
Like if anything, it's less of "This specific Religion is evil" but more "if you allow something a lot of power, there will be someone who try to use that as opportunity for some evil greed stuff", and that's something that happen to other religions too.
Now that being said, it would be sort of a plot twist if either, none in this church is actually bad guy (very very low chance considering setting of this world), or MC and co finds that some of church people that seem sus is actually good while some is actually evil/want to use MC for benefit