As you note, doctors are also licensed professionals. Should they be required to conduct operations they don't want to perform for moral reasons?
Which operations do you mean? Blood transfusions and transplants? If he does't believe in performing such operations perhaps he shouldn't be a surgeon. The government has a certain amount of leeway to regulate medicine and medical pratictioners. What if your pharmacist refuses to fill your prescription and you live 200 miles away from the next pharmicist? What if a pharmicist doesn't believe in prescription mood inhancers? Or anti-biotics--what if he's a homeopath? I see no reason why the government should not recquire pharmacists to fill out all legal prescriptions brought to them (if they practically can of course). If someone doesn't believe in birth control, I recommend fighting to illegalize it. But as long as it's legal, and can be prescribed by doctors, pharmacists--as members of the medical community--should be recquired to fill those prescriptions out.