If your beliefs, whether religious or otherwise, would put you in a position to not be able to perform the duties, then you should choose a different profession. Simple as that. If you don't want to shoot people, you shouldn't join the military voluntarily. If you don't want to teach evolution you shouldn't be a science teacher. If I don't believe any history exists before X years ago, despite scientific evidence to the contrary, I shouldn't be a historian. If am an anarchist I shouldn't be a police officer. How is being a pharmacist special? What other professions get to pick and choose when they do and don't have to fulfill their obligations, especially when these choices may have profound effects on other people? How is this different than any number of stories where someone "takes the law into his own hands" and is arrested?

Being pro-life and dispensing birth control pills is not being hypocritical, you aren't taking them. And your "choice" could be severely affecting another person's life against their free will...