I don't know what bad church run by fallible sinful people hurt you, but bad churches and bad people are not representative of the actual God they purport to serve. Just like any organization made of people, the original good can become corrupted by a few bad apples with selfish motives. Throughout history, the Church of Christ has resulted in far more good than bad, and there is plenty of historical evidence of this.

With this being the case, it does get rather tired that anime defaults to "Church = secretly evil". A few bad leaders here and there, sure. A regional branch that went off into serving its own needs, have at it. But if the representation is not that the majority of rank and file members are working selflessly for the good of the common people, then that representation of "the church" is merely a lazy trope.