I generally applaud sticking to one's guns in morally sticky situations, so I do feel like I understand both sides of the debate, here:
On the one hand, a professional dispenser of medication who considers dispensing legal drug X for its legal use to be immoral.
On the other, a prescription for legal drug X, for its legal use.
Who should win that fight? Because it's not about the pharmacist's conscience, or not just about the pharmacist's conscience, it's about the relationship between the patient and their doctor, and the patient's right to control what treatment they undergo.
An M.D. wrote that perscription. An M.D. made the medical evaluation of the patient, and determined a course of treatment, and the patient agreed to pursue it.
When that pharmacist gets in the way of this course of treatment, they are violating a fundamental liberty of the patient's to accept or deny medical care, and to control what medical decisions are made that affect them. And, in this case, as in Griswold v. Connecticut, where a state law barred prescribing contraception, to control when, and how, a husband and wife expand their family.
The pharmacist who refuses to dispense medication places themselves in the driver's seat instead of the patient, and it's the patient here who suffers as a result.
No state can take your body and force you to do something with it. Force you to bear a child, or force you to abort -- states that think 13-year-olds will make fine mommies notwithstanding. And if a *court* is going to be asked to enforce a pharmacist's right to refuse to dispense medication, that's state action thats violating the patient's substantive due process right(s), just as a court being asked to enforce a racially restrictive covenant and kick a black family out of a house they bought in a white neighborhood (Shelley v. Kraemer) is (unConstitutional) state action[*].
(If a pharmacist should have the "right" to control whether they dispense emergency contraception -- beg pardon, to refuse to dispense emergency contraception -- as their moral values indicate, should strippers who object to taking their clothes off in front of other people, for religious reasons, of course, still be paid to be strippers?)
[*] There's a difference between race and gender when conducting a due process analysis of state action. The former is held to a "strict scrutiny" standard, and the latter to an "intermediate" one, where the state must show an important governmental interest being satisfied by a method substantially related to that end. Race analysis requires a "compelling governmental interest" be satisfied by narrowly tailored means. But I'm not sure intermediate analysis is the appropriate one here. Are laws that "protect" pharmacist's values ones that classify on the basis of religious beliefs, in which case a strict scrutiny standard may apply, or ones that classify by gender?
What important or compelling interest is being upheld by permitting pharmacists to refuse to fill prescriptions? And, is this about permitting pharmacists to refuse to fill prescriptions in general, or about permitting pharmacists to refuse to fill prescriptions for women?