[Thoreau] argued that although I am under no obligation to try to fix all injustices, I am under something like an absolute obligation to not push forward things that I regard as unjust, to not participate in things I regard as wrong or gratuitously hurtful. Some doctors and nurses regard abortion in precisely this way, taught so by their religion or by their experiences. I don't happen to agree with them, but the objection is clear and principled, and it ought to be respected.
The idea that, in assuming some function -- some career, for instance -- I resign my conscience to the institution or to the state is perhaps the single most pernicious notion in human history. It is at the heart of the wars and genocides of this century and the last. It is the first -- the only -- defense in any crimes-against-humanity trial: I was just doing my job; I was just obeying orders.
I agree with the right of the individual to refuse to perform these services. But the thing is, I also agree with the right of their employers to fire their asses. If you're a high school biology teacher who happens to be a Creationist and you refuse to teach evolution, go nuts, but you are putting your job on the line and you know it. I mean, if there's a slippery-slope issue it's this one. Allowing federal protections to these employees opens the door to all kinds of other possible nightmares. Personally, I think that anti-depressants are way over-prescribed. That is my personal belief. I'm sure there are many others, likely many pharmacists, who have similar beliefs. Would these pharmacists now have the right to deny Paxil to patients? I can think of a dozen other scenarios as well.
Of course, my logic leaves open the door that a sympathetic business could allow or even encourage their employees to do this. I can easily see smaller businesses in conservative states doing this. But I'm also against using federal laws to force pharmacists to prescribe medication that are against their personal beliefs. I may completely disagree with them, but I also feel it is the right of a business owner to sell only those products he wishes to sell. It may suck to live in your small town in South Dakota, but so be it.
By the way, I'm pretty sure this same debate was essentially already covered in Clerks: