oh sorry, just re read..it was a medication prescribed by a doctor. THAT is unacceptable meddling.
From my days working in the NHS there are get outs from the equality laws which are known as GOC's- genuine occupational conditions. So for instance if you are advertising for someone to work in a pork pie factory, you can make it a GOC that they have to be prepared to handle pork. In the NHS it is mainly used where it wouldn't be appropriate for (say) a man to do a certain job an example of this might be working with very disturbed female children.
I can see where this could be used to cover pharmacists. Pharmacies dispense prescribed medicines and offer contraceptive advice (and other health advice too) not just out of the goodness of their hearts or for commercial gain but as a part of the NHS service. The NHS PAY pharmacies to do this. Now if you have an employee who is refusing to do some or all of this and there is no one else on site to do it instead, that is a breach of contract and will be treated as such.
jno is dead right, shop keepers cannot be forced to serve you but if the shop has already agreed with the NHS to do so by accepting payment on the contract then the shop owner, who may not be the pharmacist, is in breach of that contract and if I were the lady in the newspaper piece then that is where I would be taking this argument.