Of course that goes without saying. But it has no bearing on this case.
There are only two issues in a case like this -- 1) the relationship between an employer and an employee who has a "moral objection" to doing what he is told, and 2) the ability of a government to mandate business practices for private industry.
Issue #1 is clear. If the employee objects to part of his work, he should go work somewhere else.
Issue #2 does not apply in this specific case, but I brought it up because it is lurking behind all of these cases -- to the extent that the state of Illinois recently passed a law REQUIRING all pharmacies to fill prescriptions for any FDA-approved contraceptive.