"Beneficence involves balancing the benefits of treatment against the risks and costs involved, whereas non-maleficence means avoiding the causation of harm."

https://www.alzheimer-europe.org/Ethics/Definitions-and-approaches/The-four-common-bioethical-principles/Beneficence-and-non-maleficence

Beneficence: health care providers have a duty to be of a benefit to the patient and should take positive steps to prevent and to remove harm from the patient.

Consent for minors (FA2020 pg 265): Consent should be obtained from parents, except for Emergency Medicine.

This is a case where the Principle of Beneficence is given priority over the principle of respect for the patient's autonomy. In Emergency Medicine, the patient is incapacitated by the grave nature of accident or illness, we presume that the reasonable person (in this case, the patient's parents) would want to be treated aggressively, and we rush to provide beneficent intervention by stemming the bleeding, mending the broken or suturing the wounded.

So by the Principle of Beneficence, the surgery was indicated and by the same principle, the doctor proceeded without permission because it was a case of Emergency Medicine.