The Washington Post has a story about pharmacists who will not provide contraception. I don't think you can oppose these guys very strongly or make any serious argument that they should not be permitted to operate, while supporting abortion rights.
It’s worth keeping in mind that the underpinning theory of Roe v. Wade is that the government should not interfere in the exercise of discretion by medical professionals to determine what procedures are approriate to the individual circumstances of each patient.
If you believe that the government should not interfere in a doctor’s decision that abortion is the best treatment option for a patient, then I can’t see how you could simultaneously believe the government should compel these pharmacists to provide a treatment they object to as a matter of professional conscience, even if you disagree with their objection.
The professional freedom of a doctor to provide abortion is exactly the same as the professional freedom of a pharmacist to refuse to stock or distribute a particular treatment. You can support one use of the freedom and disagree with the other, but you can’t reasonably argue that one should be regulated and the other should be protected from regulation.
Pharmacists are professionals. These guys aren’t just desk clerks who hand out pills. The entry to the profession requires six years of higher ed and it’s considered a highly specialized job. The reason for this is, in large part, because the pharmacist faces issues of professional ethics and is expected to be able to make important decisions in the course of his business. These guys are highly-educated and well-paid to be a check on lying, drug-seeking patients and unethical doctors, and to catch medical mistakes that could endanger patients’ lives.
One common and extremely important example of a pharmacist using this discretion is if the same patient presents scrips from different doctors, and the pharmacist believes the doctors have not consulted with each other, may be unaware of the other meds, or that prescribed medications will have some dangerous interactions. In this case, the pharmacist should refuse to fill the scrips.
Similarly, if the pharmacist is getting a lot of scrips from the same doc for a powerful narcotic painkiller like Oxycontin, and he believes the doc is handing out the drug to people who don’t need it and should not be getting it, the pharmacist might refuse to fill the scrips.
Similarly, if patients who are not dangerously overweight are given a powerful prescription weight-loss drug, like the phen-fen/redux combo that was widely handed out in the 90's and turned out to be incredibly dangerous, the pharmacist might exercise his discretion and refuse to fill the scrips.
The central purpose of a pharmacist's job is the exercise of discretion, and while some may disagree with his use of it, his obligation is to his conscience and not to someone else's political agenda.