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From reading the NPR article, it doesn’t sound like the surgical team started the procedure. They aborted before making any incisions, which is what they should have done. The Guardian headline is a touch sensationalist.
What’s horrifying is how they got all the way to the operating room before recognizing that the patient wasn’t brain dead.
From my understanding, they won't start the procedure until the person is declared dead and the heart stops. It may seem morbid that they're waiting for someone to die, but they're not going to start hacking someone who still has a heartbeat much less is awake. They didn't "stop" the procedure because he was showing signs of life, they didn't start the procedure because he wasn't showing signs of death.