It seems to me - as a male one might say I shouldn't - that contraception is more than a religious or a woman's health issue, it is also a woman right to decide regardless of religion or health. But that's beside the point. The very fact that health is a valid element within the overall choice it remains for the employer to abstain from moral or religious judgment about a person's purpose. Freedom from religion is equally important, maybe more so.
If every possible application of the nations public funds, whether through taxation or through "premiums", are subject to the exclusion by a religious sect claims that it has a "dog in the fight" it makes public administration chaotic and unmanageable. Take for example the application of tax revenue to military. If a legitimate exclusion,  every possible use of premium or tax charge must be scrutinized for its "potential" application towards funding some sect's "religious" exclusion.