Yes, pharmacists should be allowed to refuse to fill prescriptions for the morning after pill, because for some of them, filling a prescription would be against their religion. A person should not have to be willing to assist in murdering an unborn child, just to take a job in a pharmacy.
Pharmacies can refuse fill prescriptions for the mooring after pill, only if they are private family owned a not a huge pharmacy industry like Kaiser Permanent. In the end, whatever the decision they decide to make will have an impact on their business, so it will be their business loss if they refuse the morning after pill.
Once they step into the office, they have to set aside their personal beliefs and religion and do their job. If they have a problem with their job, then they can find another one! It is their duty to serve their customers and if they have the knowledge to help someone (even if they disagree), then it is their duty to help.
A pharmacist that applied his morals to whether or not he should do his job- I.E. Filling prescriptions given by real doctors, is a pharmacist looking to get boycotted. Perhaps he should have made different decisions earlier in life, but that's completely unacceptable. In fact, I'd prefer everyone involved with my health care be an atheist.
I think the only way a pharmacist should be allowed to refuse to fill prescriptions for the morning after pill is if there is another pharmacist present to allow the sale. Otherwise the pharmacist is directly affecting the customers right to purchase the item and the pharamcist is then projecting their beliefs onto the customer, which should not be allowed.