I find it hard to believe the hypothesis -- because that's all it is, unfortunately we cannot ask the pilots what was actually going through their mind but can only formulate hypothesis -- that they went back to pulling on the stick because when they pushed the previously suppressed STALL warning became active again.
Your assumption that in a crisis situation a pilot will revert to training is false. The PF pulled back on the stick not because he was confused but because he was biased.
The 'startle effect' is an example of the over arching mental heuristic known as the
recency effect. A different but related error is the
primacy effect. The report makes clear that the pilot was primed to take the plane up because of the anxiety he had expressed about the plane's flight level prior to the incident. He went up because he wanted to go up; his training be damned.
The transcript makes clear the consistent incomprehension the PF had regarding the situation. Despite this incomprehension he still acted. He may not have acted on his training. It makes perfect sense that when confronted with conflicting and confusing stimuli he fell back on his pre-existing albeit erroneous mental model that the plane needed to go up.
You're correct, of course, that this remains a hypothesis since we cannot read his mind. Yet all hypothesis are not created equal and based upon what an extensive amount of science teaches us about human behavior it is a rational, reasonable, and quite plausible hypothesis.