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.
Medical care is highly regulated by government and there is no doubt that those issuing licenses have the power to regulate the licensees' duties as it does drug legality, purity and availability.