So sorry to hear what you had to experience and know how stressful it must have been for you, as I have had a similar experience. I echo the advice of other's here - the fact that two animals came out of brumation without problems indicates that there was some individual problem for this snake.
Reptiles have very different nervous and circulatory systems compared with other animals. Given your description of the snake before you opened the body (the flaccid body, the failure of eye pupils to constrict with bright light) the snake was brain dead or very deeply unconscious. It would not have felt pain in that state and it is probable it would never have recovered to normal function. The fact that it did not respond to coming out of brumation indicates it had serious problems!
The heart muscle of a reptile can be stimulated to contract even hours after it is removed from the body if it is kept damp in a saline solution. Any electrical and often a mechanical stimulation (touch of a sharp instrument) can be enough to jolt the nerves and stimulate beating. Heart function cannot be used as an indication of life in reptiles and your evaluation of brain function was a good basis for considering the animal dead.
I appreciate you sharing this experience for the rest of us and am very sorry that your first experience with brumation had to end this way,