Feels like we're missing a piece of the puzzle in this story. Maybe something else happened over that year? Politics? The story starts as you'd expect. Accidents happen. Support. Returning to duty. What went wrong?
Did more information come up during the time period ?
Either way, asking a pilot to not bail out in these circumstances sounds crazy.
He didn't know what was working because he didn't try to figure it out. All he did was tell the plane to switch modes from STOL to regular forward flight. He didn't see if pitch, yaw, and roll flight controls were being respected, and it doesn't seem he tried to use the backup radio, or the backup instruments, other then glancing at them.
But I don't think he made a terrible decision! Ultimately he's still alive, he healed from his injuries, and no one else was hurt, and that's a good outcome in my opinion. But maybe his judgment in a crisis situation isn't good enough for the command position he was given. He did lose a $165M piece of equipment, one that he very well may have been able land safely, and while I would never place that above the lives of actual humans, it does matter. And that's really what the three reports said: many other pilots probably would have done what he did in that situation, but he should have taken more time to ascertain whether his plane was flyable or not, even if that would have put him at further risk.
Maybe he would have been fine continuing to be a test pilot under the command of someone else's test group, but maybe his superiors decided that his actions showed he wasn't the kind of person they wanted in command. I dunno; I've never been a Marine (or any kind of military officer), so I don't know either way. But I suspect most of us here haven't, and don't really have expert knowledge on how these sorts of things are supposed to work.