After having looked at the various kinds of dark portrayals of religion in fiction, especially in the speculative genres, I'd like to circle back to what originally inspired this series of essays: the comment by John C. Wright that an actively villainous religion almost invariably is portrayed as the Catholic Church, perhaps explicitly named as such, or in a roman a clef fashion with the surface names changed. In particular, what elements lead to a Fictional Church reading as Catholic-ish, both in general and when the Fictional Church is portrayed in a negative light and thus may evoke historical anti-Catholicism.
For a concrete example, when I was writing a critical essay on Ben Bova's
Mars Life, I commented on how his fictional New Morality seemed to be meant to evoke the Moral Majority of the 1980's -- yet its leader was styled an Archbishop and had people kissing his ring in the manner of a Catholic archbishop. In this novel, the New Morality was an antagonist but not an actual villain -- rather than being an Evil Church of Evil, they're more on the order of misguided: technophobic in the manner of many Protestant faith communities that practice Biblical literalism and young-Earth Creationism, and promising Answers to frightened people in a very uncertain time of climatological upheaval. Furthermore, they co-exist with an explicitly identified Catholic Church that is presented positively, with a Jesuit scholar making several of the key breakthroughs in understanding the language and culture of the long-extinct intelligent Martians.
To me, the portrayal of the leader of the New Morality in Catholic terms was actually more jarring and damaging to my suspension of disbelief because my own religious background is closer to that of Jerry Falwell and the other leaders of the Moral Majority. So I was trying to figure out how the heck someone from a church with an episcopal polity should've become a leader of an organization I would associate with churches that are largely congregational in organization, who are associated with the publication of the series of thick pamphlets known as The Fundamentals around the turn of the last century, and have a long history of viewing the Catholic Church as un-Biblical in doctrine and practice, particularly the hierarchical and monarchial elements of its organization. I would've expected someone more like Falwell, dressed in a suit and tie, formal but in a presidential manner rather than the monarchial manner of Catholic hierarchs.
For me, it was primarily a problem of suspension of disbelief, based upon what I knew of the faith communities that were most likely to produce an organization like Bova's New Morality. The Archbishop and the people kissing his ring felt like an unthinking application of Catholic imagery to a completely different Christian faith community, a perfect example of the trope of All Christianity is Catholicism and its problems. Knowing that Mr. Bova was an atheist, and not knowing what sort of exposure to religion he might have had in childhood, I was willing to give him a pass. But I really would've liked to have seen some awareness of the rest of Christianity, and particularly the various congregational faith communities, such as the Stone-Campbell Restoration Movement or the various Baptist Churches.
Which means that at least some authors who create a fictional Evil Church of Evil may not even realize that their portrayal is reading as anti-Catholic -- or even realize that certain details of their villainous Fictional Church code as Catholic, even in a completely imaginary Secondary World where Christianity is not present. Yet avoiding creating such a Catholic-ish Fictional Church may not be easy, for the simple reason that if you're going to have a truly dangerous Evil Church of Evil, rather than a bunch of nuisances scattered around, you're going to need a lot more organization than a network of independent congregations, even ones that have been systematically infiltrated and corrupted, can muster. Merely avoiding terms such as "pope" and "bishop" or ceremonies such as the kissing of the ring may not be sufficient to avoid a Catholic-ish feel to a villainous Fictional Church which has layers of hierarchy and of bureaucracy, elaborate liturgy and vestments, and imposing buildings.
One of the best ways to avoid inadvertent offense is thorough research on the Primary World faiths that may be deliberate or unconscious models for one's Fictional Church. Not just specific "how do they do this" research, but immersive reading that goes beyond the surface appearance to apprehend the religion as a living tradition and faith community. Read primary sources by members of the faith community, whether born into it or converts, and by people who have left it, whether by deliberate rejection or through a gradual drifting away.
And even if you're a pantser who discovers that you've written a Villain Church that could be interpreted as anti-Catholic (or prejudical to any Primary World faith tradition -- particularly in our post-10/7 world, awareness of common anti-Semitic tropes and images is wise), it's not necessarily going to mean you have to 86 the entire work. As Mr. Bova's work shows, a positive portrayal can go a long way to counter the appearance that your Fictional Church is a roman a clef attack. Similarly, in the Belisarius series, Eric Flint made it clear that the Malwa villains' form of Hinduism was not a smear on Hindus by showing Hindus that disapproved of it as an aberration from tradition -- and in the final volume, they have their role in bringing down the Malwa and the time-traveling AI that was the author of their corruption. Even in a completely Secondary World fantasy, these techniques can be employed to reduce the likelihood that your Fictional Religion will be seen as a slur on an actual religion -- and will have the additional advantage of richer worldbuilding, and a sense of history to your world, that the religions are rooted in the cultures and societies rather than just pasted-on local color.