I'm trying to determine if there is any actual science behind the "his brain has dissolved so he can't experience pain so there is no suffering to be ended" line of reasoning. I can't find any support for this countering premise that pain is entirely confined to the brain, so it seems like nothing more than a convenient claim on a position that is just "not provably wrong" rather than a position that has any reason to accept as right.
I think I understand.
In the course of your research, you're going to become involved in the spinothalamic tract (the names in neuroanatomy often make sense once you crack the language. This pathway goes from the spine to the thalamus). Now, there are many types of pain, but most of nociception eventually ends up in the thalamus (which is inside the brain, but is kind of a gatekeeper between the cortex and the rest of the body). Near as anyone can tell, 'consciousness' is contained within the interactions between and within the thalamus and the cortex.
So, there are two ways to prevent a noxious stimulus from 'causing pain'. One is to literally interrupt the pathway. If that interruption is 'higher up the stream' than the reflex action, then you can still have a pain reflex without actually experiencing pain. The second is to not have a functioning cortex (or thalamocortex system).
Now, evolutionarily speaking, 'reflexes' are buried deep in our neurodevelopment. A bazillion and one animals have amazing hardwired reflexes built into their early development. This is why we can breathe so quickly after we're born. They also develop earlier during fetal development than functions associated with actual cognition. You need a cortex to experience pain. You need lower systems to respond to painful stimuli.
Because of the importance of nociceptive reflexes, I'd not be surprised if those pathways were also more hardy (for lack of a better word) as they travel up the brain into the cortex itself. The articles talk about how heavily degrades Alfie's thalamus was, but I wouldn't know (and doubt the neurologists would know, either) which areas of the thalamus were being degraded preferentially. I'd certainly not bet against 'pain' being one of the last to go, if we were to place different thalamic functions on some type of spectrum of likelihood.