I don't believe in the use of force, except in self-defense. I believe people should have the right to practice their religious beliefs, or even their ethical beliefs, within reason. However, there is an important factor in this situation that needs to be considered. Pharmacists are licensed, which is to say they have a monopoly on the dispensation of medicines. The government licenses them, and uses force against anyone selling prescription drugs without a license. The licensing limits the supply of pharmacists, thus raising the profitability of pharmacies and the pay of pharmacists, whether they are employees or own the pharmacy.
To accept the money, and accept the help of the government in jailing the competition, at minimum pharmacists should have to accept that they will fill any prescription written by a doctor and carry any non-prescription drugs approved by the FDA that are in demand by the public.
Consider some variations on this theme. Suppose a racist pharmacist refused to sell drugs to people of other races. Would we tolerate that? Suppose a pharmacist has stock in a particular pharmaceutical company and refuses to sell medications manufactured by rivals. What if a pharmacist denied drugs to people of rival faiths who came into the pharmacy? What if a pharmacist thinks it is a sin to dispense drugs for HIV?
The sale of pharmaceuticals to the public is now dominated by large chain stores. It is a highly profitable business. You cannot buy medications in the U.S. without a prescription. The government tries to prevent you from importing identical, cheaper, medicines from Canada or Mexico.
So my solution, could the Herculean task of getting such a reform through our corrupt political system be accomplished, would be to allow any business to sell prescription drugs, as long as they required no formulation. Then pharmacists who subscibe to a particular faith could let that be known and help only the customers they want to help. I would also make most presciption drugs available over the counter. That would greatly lower the cost of medicine in the United States.
Under the current regime, the only real test of a pharmacist's faith would be to resign rather than sell morning after pills. Anyone can act like a jerk and tell themselves they are "better," than other people. Going out and getting another profession, that would show some real backbone, which I would admire even though I do not think the morning after pill is a sin or evil in any way.