SNS
I don't know much about flying (only a few hundred hours in VMC), but I know quite a lot about human behaviour and learning.
I can understand why the ab initio training focuses on operant conditioning (that is teaching a response to an event), since I guess the logic is that people with little experience will likely freeze under stress unless there is a clear, programmed response to the stimulus.
No doubt in the early days, if one takes a hard pragmatic view, fewer people die that way.
I can also completely relate to your view that the same conditioning can kill people.
Perhaps the challenge is how to handle the crossover stage, e.g. the point at which the pilot has enough experience to start to think clearly as you decribe.
My impression is that, post PPL, there is little support to encourage that decision making and the only contact most PPLs have with an instructor is for a biennial, where they are taken back to the PPL 'learning by rote' responses.
Therefore, I think that we owe Chuck a vote of thanks for raising this subject and also to the other contributors who have shared their greater experience to help the many on here expand there horizons
