The issue is immensely complex, to say the least. However, at the end of the day, medical treatment options ought to be decided by the patient, or by somebody who has legal guardianship, and the best interests of the patient in mind.
While this decision is certainly controversial, I very much doubt that it was taken lightly. And all healthcare workers will increasingly be faced with ever more complex ethical issues. To some, euthanasia and abortion procedures are perfectly acceptable. To others, they are tantamount to murder. Personally, I of course have my own views on these issues, but I cannot force these views upon my patients, just like I can't force a patient to undergo, or refrain from, specific treatments.
Of course, some current and future procedures are so controversial or ethically complex, that physicians should or will have their own personal opinions about them. And I think it's every physician's right to abstain from performing procedures s/he deems unethical. Thus, I fully support any physician who for instance refuses to carry out abortions on ethical or religious grounds. But just as that physician shouldn't have the power to ban such procedures, physicians shouldn't make decisions on bahalf of patients or guardians, who are capable of making informed decisions on their own.
Of course, the procedure in question here could be construed as a violation of the "do no harm" part of the oath we've all sworn to uphold. Yet the same applies to euthanasia and abortions, among other procedures.
At the end of the day, we must all strive to help patients and their families in the best way we can. And that will, invariably, increasingly raise ever more troubling ethical questions. These should be debated openly and frankly among medical practitioners, patients and society, but it is wrong to assume that any clear answers can be found.
Personally, I initially found the story referred to here troubling. However, I do feel that the parents have a valid argument. As to the question if I personally would participate in the procedure, I think the honest answer right now is that I simply do not know.