I brought up Scientologists as an example because I, personally, would feel extremely uncomfortable spending lots of time in the company of one and having to rely on them.

As a casting director, I imagine I wouldn't have to personally deal with the Hubbardite much longer, so that issue would not arise. I would, however, try to evaluate the risk of the film being harmed as a result of this trait of the actor - say, if other, more important members of the crew had similar reservations as mine which would prejudice their work; or if the actor became unreliable, cumbersome, or quit altogether due to Church obligations; or if he were [made] to spout Scientologist propaganda during interviews; and so on. So I guess I would hold it against them, although not being familiar with how cinema works I can't say to what degree.