I'd guess that professional opinion is divided on the optimal way to rehab following MFS and I'd also guess that doctors and trainers involved with professional athletes tend to be on the more aggressive end of the spectrum - since time is money.
In my own experience with physical therapy, I'm amazed at what excruciatingly painful things the therapists do to you - a level of pain I'd never be able to inflict on myself. So my body was telling me it was the wrong thing to do, yet it seemed to be as beneficial as the therapies were successful.
But, I'm not in the camp that says Amare did the wrong thing, whatever it was, because he seems to have recovered as much and as fast as anyone has from MFS - convincing evidence that he did the right thing. What it makes me think is that if someone else is doing something painful to you, its different than doing something painful to yourself - you'd probably unconsciously change what you're doing to lessen the pain while a therapist would not.