How is this argument different from the arguments of people who want to draw the line at hiring transgendered people or hiring women or hiring people who are over 6 feet tall? The only material legal difference, as far as I can tell (IANAL) is in whether you are discriminating against a protected class or not, and what constitutes a protected class seems to be largely a political decision. And religious affiliation is definitely explicitly protected.
These are, of course hard issues. It's _hard_ for all of us to not discriminate against people based on our prejudices. For you it seems to be hard to not discriminate against Scientologists. The right moral response is to realize your prejudices and fight them. The laws actually make that a bit easier in some ways (e.g. it's illegal for you to ask prospective job candidates whether they're Scientologists).
Whether it's a social fit problem depends on two things. The first is whether the person's private beliefs affect their workplace behavior. Obviously in some cases they do and in others they don't. People are pretty good at compartmentalizing.
The second social fit problem is whether the person's co-workers are so outraged by the fact of the beliefs existing (or the person's gender being "wrong" or their hair being red, or whatever these people happen to have personal hangups about) that it affects _their_ behavior. This is pretty common, obviously, and the fault in such cases lies in the co-workers not the hire. There may still not be a good "social fit" as a result, but this situation is cause to look long and hard at the "society" that's not being fit into...
I would like you to also consider a concrete example. You say you won't hire a believer in alien abductions. Would you hire a "tin-foil-hat" type who believes the NSA is spying on everyone? Would you have hired such a person two years ago, or would you have considered them paranoids whose "thought patterns and general mental stability" would preclude a good "social fit"? Clearly your priors have updated since 2 years ago, but it's always worth evaluating whether your priors might be wrong and whether a reasonable person might come up with different priors.