Its just that one asshole priest(bishop?) who lost his marbles fucked everything up.
Well... Only one non-name minister was "good" who wasn't part of the church but was simply ordained.
Outside of that we have one Archbishop who is evil and is hinted to be a rapist. A Bishop, soon to be Pope, who advocated genocide. All the priests actually shown. Twats in a bar.
One of the characters who explicitly worked for the church has been rewritten to not and is now part of a non-religious group of science and reason against religion who are persecuted by the church. The Church's active participation in the story has been written out for a narrative where they are trying to purge the sinners (Which isn't ENTIRELY inaccurate, but in a weird twist the games had more nuance)
They also rewritten another character who had SOME religious affiliation to have none and have no religious attitudes, in fact anti-religious attitudes.
It is more that anyone who is religious in this show so far is evil... and anyone who out specifically non-religious (or anti-religious) is good. Even to the extent of rewriting characters to accommodate this shift.
It is a WEEEIRD juxtaposition for Castlevania.
It would be like if they made an Adaption of Harry Potter where anyone who likes magic is evil... and only people who want to stop magic are good... And they rewritten Harry Potter to be the most anti-magic person around. It isn't a bad idea for a book it is just weird for a Harry Potter adaptation.
Maybe I am wrong and Belmont is actually religious and a future episode will demonstrate this.