To me, it's according to the situation. If it is a privately-owned pharmacy, then they absolutely have the right to refuse service based on whatever they want to. It's their business, and if they lose business based on their beliefs then they are the ones that suffer. Also, pharmacists are extremely liable for the drugs that their customers receive regardless of who prescribed it.
For example, my wife's obstetrician in Atlanta will NOT prescribe the pill for whatever reason. He is pro-life, period. He says (which I have no proof) that there are always better ways to treat the problems that girls always say their on the pill for.
Now, does he lose business because of this practice? Absolutely. But, on the flip side, that is why my wife wanted to go there even though it was an extra 20 minutes each way. He practices his profession with the Catholic faith in mind. You must remember that my wife is much more hardcore than I am, but I am glad that we went to him because we learned a lot.
I think people forget that many of these cases pertain to an individual's business. As long as they are not breaking any laws or endangering someone then they should be able to run their business based on THEIR beliefs. I don't see how someone could disagree with that.
On a somewhat related note, is the way states are dictating whether or not patrons of a bar can smoke or not regardless of what the owner wants.