With all due respect, I think you are taking choice or preference and mistaking it for discrimination.
Discrimination is simple. Example. You own a store, and you do not allow Catholics to work in, or shop in your store. That would clearly be discrimination on the basis of religion. Preferring not to associate with Catholics because you are not one is not in and of itself discriminatory, as I think you are saying it is. It is a choice based on personal preference. When you speak about a business on the other hand, it is discriminatory to selectively hire applicants based on their religion, even if you own a Catholic Book store.
The thing is this. Some applicant might be of another religious persuasion, or none at all, but they know how to put books away, how to ring up sales, how to treat customers with respect, they are honest, trustworthy and reliable. So, there is no basis on which you should be able to deny them employment based on their not being Catholic.