The refusal of some pharmacists to fill some prescriptions based on religious belief is an ethical dilemma. On one hand, forcing someone to do something that is against their moral standards is repugnant. On the other, by refusing to fill prescriptions, these pharmacists are essencially making medical judgments. They are, in effect and fact, refusing to dispense prescribed medical treatment. They are providing an unqualified second opinion to a doctor. (I think it's safe to assume most pharmacists are not licensed doctors. Even if they were, it would be an unsolicited second opinion.)

If the ethics of dispensing ALL drugs is disturbing to these pharmacists, it may be possible they should rethink their choice of career. The following is from a Washington Post article Pharmacists' Rights at Front of New Debate (subscription required):

An increasing number of clashes are occurring in drugstores across the country. Pharmacists often risk dismissal or other disciplinary action to stand up for their beliefs, while shaken teenage girls and women desperately call their doctors, frequently late at night, after being turned away by sometimes-lecturing men and women in white coats.

"There are pharmacists who will only give birth control pills to a woman if she's married. There are pharmacists who mistakenly believe contraception is a form of abortion and refuse to prescribe it to anyone," said Adam Sonfield of the Alan Guttmacher Institute in New York, which tracks reproductive issues. "There are even cases of pharmacists holding prescriptions hostage, where they won't even transfer it to another pharmacy when time is of the essence."

That is what happened to Kathleen Pulz and her husband, who panicked when the condom they were using broke. Their fear really spiked when the Walgreens pharmacy down the street from their home in Milwaukee refused to fill an emergency prescription for the morning-after pill.

"I couldn't believe it," said Pulz, 44, who with her husband had long ago decided they could not afford a fifth child. "How can they make that decision for us? I was outraged. At the same time, I was sad that we had to do this. But I was scared. I didn't know what we were going to do."

Slight Addendum: Media Matters for America has more background and examples on this issue at Who are Karen Brauer and "Pharmacists for Life"?