Another GP here. I prescribe all contraception. In our area, we do not refer for termination; the local system allows us to give the necessary information to the patient and she then self-refers. This avoids any problem with doctors' personal views.
However, while I think the service OP received was poor in that she had a 45 minute wait, she was not actually denied contraception. The system worked (albeit with a delay). I suspect the practice was unaware that the locum had this personal issue with contraception, but if they were aware then this should have been made clear to all the patients seeing that locum.
I absolutely agree that doctors should have the right to opt out of providing termination; even gynaecologists can do this. The result has been that these services are largely removed from general hospitals now, and are provided by specialist services. The imperative, however, is that this must not result in a delay in treatment for women requiring the service.
NB The doctor signing a prescription, no matter who wrote the prescription, is legally responsible for it. Thus as independent practitioners, doctors have every right to refuse to sign any prescription if, for example, they do not believe that it is the right drug for the patient, or if they do not have sufficient experience with that drug to be able to take full legal responsibility for it. This is true of all drugs, and contraception is no exception. Also GPs do not have to provide contraceptive services at all (it is not part of the core contract), although most practices choose to do so.