It's already been done in the original DG - see '"The New Age" by John Tynes. Certain DG authors have basically admitted that the Enolsis Foundation is supposed to be the Church of Scientology.
Unfortunately, it's not a good idea to do a a scenario that explicitly involves Scientology by name. The Church of Scientology is extremely trigger-happy and petty when it comes to lawsuits. A scenario about Scientology could never be published, and it seems like Caleb is moving into mostly running games that he writes for publication. Even if he never published the scenario but just posted it on RPPR, I'd say there's still a small amount of risk, at least if the title or description text mentioned Scientology (obviously, they don't have people to listen to every podcast in the world and watch out for negative references).