glands on strike
I don't think any of these answers address the OP's question, which I think is an interesting one: we know people do burn out, and we may agree that it's common for someone who trains really hard to fall apart, but we haven't really gotten to the core of why this happens. If you look at Hall and others in that situation, they're relatively uninjured, they're now well-rested in the sense of getting plenty of sleep and taking plenty of easy days, they're obviously not short of glycogen in their bodies, they look OK, and I believe they're still motivated. Even if Ryan Hall wasn't motivated, but was still putting in the miles (as he was), you'd think he'd only slow down a little bit, and still be able to run 2:10 to 2:15 or so. But I get the impression he'd be lucky to finish a marathon in 3 hours now.
I don't know the answer, but I think that is what the OP was getting at: we have these terms, like "burned out" or "toast", or even more sophisticated terms like "cellular damage", but we don't really know what it entails. Like, what do you mean, cellular damage? Is it something you can see under a microscope?
I'm also curious about what goes on physically in these cases. My own experiences are enough for me to fully believe that it's not just "mental" (I put the word mental in quotes because, maybe it is mental in the sense that the brain refuses to allow the muscles to work hard any more, or something like that - but not mental in the sense that you've become a big wuss). I suspect it is more of a hormonal thing. This seems especially likely for Hall, given his thyroid problem.