If a doctor decides that they will not perform certain procedures, how can that be compared to any form discrimination? The doctor in is no way excluding groups of people from offered services. In the case of doctors who do not want to perform abortion, they do not exclude any woman from services that the doctor does offer.
The real question is, do doctors have a right to choose what types of services they offer? All other professions, that I can think of right now, can choose what services they offer within their sphere. Lawyers, for example, can choose what types of cases they will take. What is the trouble with doctors?