So, just out of curiosity: Just how old is "Church is Evil" trope in Japanese media, and where exactly did it originate?
Historically, Japan has had a pretty tumultuous relationship with Christianity- Catholic missionaries from Europe had more trouble converting the Japanese than they did with people of other nations, owing to the highly-entrenched nature of both Shintoism and Buddhism, as well as the nature of Japanese as a language quite different from, say Indian languages (you'll have to read up on Francis Xavier for more details, since he was one of the primary missionaries involved in both Japanese and Indian conversions). Even after they got some conversions carried out and won Oda Nobunaga's favor, the religion was seen with considerably more suspicion by Toyotomi Hideyoshi and the Tokugawa Shogunate, to the point where it was banned as threat to national unity. Christians and Catholics were publicly murdered and even crucified, with the luckier ones only forced to convert, and later on, the Shimabara Rebellion only led to more oppression. After Japan opened up in the Meiji era, the religion was unbanned, but there was this general sense of bitterness and suspicion about the faith prevalent in the country. It was seen as a sign of colonial Europe, being thoroughly anti-traditionalist and alien. The westernization of later eras did soften these suspicions, especially since churches and Catholic schools started to be established and were often seen as places of high culture and prestige (you can see hints of this in Class S stories).
The point of all this is that Japanese media has an extremely odd, almost-contradictory view of Christianity- they adore the aesthetic and love to appropriate the symbols and terminology because it sounds exotic (as seen in everything from Neon Genesis Evangelion to Seraph of the End to Bible Black). There's generally little regard given to accuracy or history, because the Church embodies the aesthetic of aristocratic, rich Europe, while also being considerably more disciplined and mysterious than a standard monarchy. From a narrative standpoint, you can do a lot with churches- everything from ninja-monks to secret angels to chained-up gods. They've got fixed ideologies, a clear cultural association, and are what you might call 'stock institutions' in the same way as you have pseudo-Nazi governments or pseudo-Victorian societies- no actual historical context is dropped, but if you see a militant racist with an armband or a baroness in a frilly dress, you generally know what to expect. Audiences are saved the effort of needing to think about what a character might represent or contemplating the political ramifications of their existence, because they know that the pseudo-Nazi is a dick and that the pseudo-Victorian is stuck-up, just as they know that the pseudo-priest/nun is dedicated and possibly fanatical underneath a façade of kindness.
The Church being evil is, as Throbelisk above pointed out, a very realistic trope, and also your basic 'everyone apart from the characters saw this coming'-type of subversion. The audience expects the Church to be evil the moment they see a priest grinning sinisterly or spot a nun beating up a choirboy, so they're spared the effort of debating the ills and benefits of religion and can just eagerly anticipate the moment where the veil comes off.
TL;DR- Part of it is just good old-fashioned religious scepticism that you commonly find in modern stories, where anyone who's super-devoted to any kind of faith is assumed to be kooky; part of it is Japan's weird love for European aesthetics versus their disdain for European society; and part of it is just because it lets you simultaneously set up and invert a status quo without actually needing to do much worldbuilding, since you've already established the three-act structure of your story's evolution- Act One, the church rules, Act Two, the church is revealed to be bad, Act Three, we take down the church and build something new. I do wish that stories actually delved into what made churches work in the first place, though- they wouldn't be so powerful if they didn't offer large groups of people legitimate inspiration and faith. There's just so much ground to cover- optimism decaying into scepticism, debates over the idea of evil, the doctrine in scriptures versus the truth, the corruption in higher echelons versus the faith of new acolytes, and a million other fascinating topics, but nope- your standard Japanese story just makes churches shady from the word go, and only uses them to give characters Bible-themed superpowers so they can brawl things out on a chapel in the final chapters. But I guess that's what people expect and want- boring debates on theology in dusty libraries between disillusioned monks would probably be less entertaining than a plan to use Satan's femur to shoot God in the throat.
