The right of a professional to refuse a service based on religious objections is a complex issue and only growing more so. 

Obviously, conscience should be respected in situations where a person is asked to directly participate in something they find morally objectionable, like a nurse assisting in an abortion. 

But on the other end of the spectrum are things like bakers refusing to sell wedding cakes to gay couples, an act that's completely immaterial to gay marriage itself. (As I write this, the Supreme Court has just agreed to hear one such case.)

You can make a sound argument for a pharmacist refusing to sell abortifacients. But should that extend to contraceptives too? And, if so, should condoms be included? As long as we're talking about not enabling bad behavior, should merchants be allowed to refuse the sale of cigarettes and liquor to adults, even though those things are legal?

These are not easy questions and there is no one-size-fits-all answer.