idk, the archbishop doesnt seem like a typical evil church guy, maybe he is searching for witches not for killing but for request something, anyways it feels like it wont be a problem
Imagine how fucked they would be if they decided to brand the place as evil.
Nobu is literally being actively protected by a goddess, and regularly visited by the shrine maiden (fox)
but realistically speaking, it would indeed fucked up. But Idk, if you refer to another (many) Isekai genres, another world has another god/s. So maybe the shrine maiden is doesn't have any power/authority over another world.