Freedom of religion is not the freedom to become a pharmacist and then deny patients legally prescribed medication because of your personal moral objections to the patient's life choices. That's not freedom of religion. That's the freedom to oppress others ... sorry, fundamentalists, you don't have that right.
Now, to me, the obvious solution for a person who has moral objections to the job description of being a pharmacist would be to not become a pharmacist, but that solution doesn't seem to present itself to these pharmacists. I say we help them out.
I'm not sure if there already is, but there should be some sort of pharmacist equivalent to the American Bar Association which can de-license pharmacists who refuse prescriptions for illigitimate private reasons. This is a necessary step, because if we grant personal faith as a legitimate reason to refuse to fill prescriptions, then we are granting pharmacists the right to refuse to fill any prescription for any reason. When people's health is at stake, that is unacceptable.