In the following article, I will be focusing on Christian SF&F, but this argument is valid for any ideology based subgenre.
It has been mentioned that Christian science fiction and fantasy ought not to be considered a subgenre of SF&F at all. It is, after all, associated with a particular ideology and/or belief system. Might as well have subgenres called Taoist SF for Ursula K. LeGuin’s work, or Muslim SF, should such ever appear on the horizon. And to an extent, this is a valid argument. If we allow one particular religion, ideology, or belief system to have its own subgenre, then, to be fair, we must allow all to do so. The current classification system within SF&F, while often generating controversy, still generally classifies its works based on setting and content, not ideology or belief system. So ideology based subgenres are still something of a bastard child in the way books are classified.
For instance, Steampunk is a genre that contains certain elements within it’s setting and characterization that do not apply to sword and sorcery, and this is as it should be. The same is true for epic fantasy versus hard SF. Even if we haven’t truly codified the system completely due to its changeability, its ability to adapt to new writing styles is part of what we love about it.
But, for all of that argument’s validity in a logical sense, there is another to be made, which I think is much more pragmatic. That argument stems from categorization as defined by marketers. Sure, some purists out there will decry this notion as absurd, since it is the fans and writers who should define the genre, not the marketers who can justly be accused of not understanding the intricacies of SF&F. But hear me out.
“Marketers and publishers” classification is how book sellers know where to put a book on their shelves. When laying out their store, many of the books are placed in locations relating to where the publisher believes a book should go. That is why Harry Potter, although popular with adults, is found in the children’s section. Its publisher, when putting out the first book, decided that was a logical place for it to go. For that same reason Madeleine L’Engle’s AWrinkle in Time, originally written for an adult audience, landed in the children’s section because of a marketing decision. She makes such a claim in her memior A Circle of Quiet. In early 1960, the book had received a long series of rejections, “because it deals overtly with the problem of evil, and it was too difficult for children, and was it a children’s or an adults’ book, anyhow?” writes L’Engle. Her marketer ultimately decided to market this book for children, and a Newberry Award was the result. That is why Tolkien, while popular with kids, is more often found in the adult fiction section of the store. He was marketed that way at first, and so he continues to be. These classifications are not wholly arbitrary, and certain conventions are used, but ultimately the publisher and its marketing team decide where the book would best sell, and the bookseller follows their lead.
So, what does that have to do with Christian SF&F? Well, as any customer in a bookshop knows, there is often a section devoted to Christianity as a whole. This is intentionally designed to allow readers of religious works, including fiction, to choose books that follow this belief system, in its myriad forms, and to easily find books that agree with their assumptions and presuppositions. Additionally, it is such a large market that to the bookseller it is worth the effort to differentiate it from the general fiction, much like Science Fiction and Fantasy has its own section as well. Other sections that are comparable would be the section on Women’s Studies, or that on Gay, Lesbian, and Transgender Works, or on Minority Works. These are worthwhile categorizations for the marketer and bookseller as it allows potential customers ease of access. They allow readers to find works they are looking for easily and in a subject that interests them.
Each of these larger genres must then integrate with others to create subgenres. That integration only enhances the ease in which a reader can find a book of interest. For example, Women’s Studies finds itself turned into a subgenre in the general fiction genre, often called feminist fiction. In Science Fiction and Fantasy, there is a small, but growing, idea of a subgenre known as feminist SF. Usually written by women or about women’s issues, this is a subgenre that is intimately related with its non-fiction counterpart. And noone seems to have much trouble agreeing that feminist SF is a valid subgenre. Gay, Lesbian, and Transgender Works also has its subgenres, particularly in the romance section, as well as a growing subgenre in SF. Both of these examples are subgenres which are based on ideology, which relate to a larger genre, and are accepted by retailers and publishers alike.
Therefore, if there is such a thing as a Christianity genre, then when it appears in the SF&F genre its subgenre must be that of Christian science fiction and fantasy. By relating an existing, larger genre to a smaller subgenre, we show its validity and provide ease of access to customers looking for a particular work. You may find argument with the existence of that overarching genre, but precedent stands against you.
In essence, Christian science fiction and fantasy is a valid subgenre, as are any subgenres based on ideology as well as setting. Obviously, if you allow one (as we already have with feminist SF) you must allow them all. But that only adds to the diversity that makes SF&F so great in the first place. Christian SF&F is a valid subgenre, as is feminist SF, as would be Taoist or Muslim SF. To say otherwise feels more like close-mindedness that the spirit of freedom that SF&F has always fostered historically.
For a perspective from someone not a self-pronounced Christian, read this piece at The Guardian that argues that lesbian fiction is a necessary and needed categorization.

>Christian science fiction and fantasy is a valid subgenre
Absolutely. I think some niche markets, such as Christian and science fiction romance (well you knew I was going to mention that!), are maligned for whatever reason. I mean, I know the reasons but there’s no need to air a laundry list.
Yet the rejection exists despite the fact that there are millions of readers who all want something different. Why not give it to them? The more the population grows, the more diverse SF is going to become. It’s already started anyway. Let’s celebrate that.