While I am normally quite libertarian in my feelings, I guess I don't see this as a simply 'their business, their rules' situation.
As a medical professional, my first duty is to serve my patient. Not to impose my moral system on them. It's what we call the principle of autonomy. That part of my job is to inform the patient to the best of my ability and allow them to make the decisions regarding their own person. I certainly agree that this should be balanced with my rights not to do anything morally repugnant to me. However, when someone places themselves in your care, they are giving you a very special sort of trust. This is not just a theoretical concern, it's something that has to be put into practice on a daily basis.
So, as a health care provider, I believe I have a duty to inform my patient of every alternate means of treatment. I also have a duty to give them the information they need to get that treatment if they wish and a duty not to hinder that.
In the case of the morning after pill, which frankly doesn't work all that well at baseline, the efficacy sharply decreases the longer its administration is delayed. So I think when appropriate, the physician has a duty to inform the patient it exists, ascertain if they want it, and get them as quickly as possible under the care of someone who will dispense it if they so wish. Not mentioning it is deceptive. Delaying it's administration or hindering a patient's obtaining it is a manipulation of someone who has entrusted their care to you. It's not wrong for the doctor to adhere to their own beliefs, it is wrong to use deceptive or manipulative means to force the patient to adhere to those beliefs as well.
To give a really personal example, almost 60 years ago my grandmother went to a doctor in order to terminate a pregnancy. She was given a placebo, and by the time she figured that out it wasn't safe to use another method. Even though if she had gotton her wish, I wouldn't exist, I still find what the doctor did abhorant.