I believe them when they say that they were looking more broadly at religion and peoples beliefs then dissing Scientology specifically. It's hardly far-fetched, evil cults ruining everything by dealing with forces they shouldn't has been a horror staple since the dawn of time. Sure, Unitology does remind you of Scientology in general feel, but the blame for that lies firmly on Scientology. If you make something crazy, written by a science fiction author, then you are going to seem similar to other crazy science fiction.
I don't blame the developers for distancing themselves from Scientology criticism. They are busy people. They have things to do besides criticize Scientology. Just because we like seeing people stick it to Scientologists doesn't mean they have to drop everything to criticize them too.