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This isn't so much like a Muslim bartender refusing to serve alcohol, since there are so many thousands of other kinds of prescriptions a pharmacist could actually fill. This is more like an Orthodox Jewish butcher refusing to serve pork.
That said, an Orthodox Jewish butcher would probably be working at a kosher shop. If these guys don't want to sell birth control, why don't they just start their own pharmacies and run it however they want. Those of us who aren't interested in supporting their cause can get our prescriptions filled elsewhere.
That probably means those people won't be getting jobs at all those small town Wal-Marts, but you don't hear kosher butchers whining about their job prospects needing protection from being geographically limited.