More on the New York contraception-mandate case

Here (thanks to Professor Friedman) is commentary on the decision by the New York Court of Appeals upholding that state's narrow religious-employer exemption to its contraception-coverage mandate.  The commentary includes a line from the opinion that I had overlooked: 

"[W]hen a religious organization chooses to hire non-believers it must . . . be prepared to accept neutral regulations imposed to protect those employees' legitimate interests in doing what their own beliefs permit," Judge Smith wrote. "This would be a more difficult case if plaintiffs had chosen to hire only people who share their belief in the sinfulness of contraception."

Why, exactly, is this true?  That is, why should a religious organization's decision to "hire non-believers" require it to compromise its identity and commitments?  It seems to me that this line of reasoning would have dramatic effects on, say, Catholic universities that (a) are committed to being meaningfully Catholic but who (b) believe also that their Catholic mission is enhanced by the presence of engaged, sympathetic non-Catholics.

Also, Eugene Volokh has some thoughts about the court's standard-of-review ("mystery scrutiny") in state-constitution free-exercise cases.