I think this is a more subtle question than it appears on the surface, especially if you don’t think of it as a one-off.
Whether or not Scientology deserves to be called a “religion,” it’s a safe bet there will be new religions with varying levels of legitimacy popping up in the future. And chances are some of them will have core beliefs that are related to the technology of the day, because it would be weird if that weren’t the case. “Swords” and “plowshares” are technological artifacts, after all.
Leaving aside the specific case of Scientology, the question becomes, how do laws that apply to classes of technology interact with laws that treat religious practices as highly protected activities? We’ve seen this kind of question come up in the context of otherwise illegal drugs that are used in traditional rituals. But religious-tech questions seem like they could have a bunch of unique wrinkles.
I was impressed by an earlier mod along similar lines, Portal Stories: Mel. Hope this one is as well-done.