You're not likely to find a remotely reasonable hypothesis, even in the Methodsverse where magic abounds, by which the internal parts of a thinking computation can be damaged by damaging the brain, and yet removing the whole brain leaves the soul capable of internal thinking.
Has your hypothesis that thought remains possible after the whole brain has been removed, in fact, been tested?
EDIT: I read your post as meaning that the "fact" that thought remains possible after a brain has been removed [to be cryo-frozen, for instance] was evidence against a soul.
No plot spoilers here, just wanted to flag a bit of poor reasoning that shows up in Chapter 39:
This is a surprisingly common fallacy. Just because X depends on Y, it doesn't follow that X depends on nothing but Y. A phenomenon may involve more than just its most obvious failure point.
To illustrate: Suppose I'm trapped in a box, and my only way to communicate with the outside world is via radio communication. Someone on the other end argues that I don't really exist -- "There's no person beyond the radio receiver, for if there was then there wouldn't be any such thing as damaged radios!" Pretty silly, huh? But people say this kind of thing in defense of physicalism all the time.
(N.B. This is not to defend the existence of souls. It's just to point out that this particular argument against them is invalid.)