The writer has made an illogical jump, trying to apply the Sensei's statement to encompass the whole art."

Obviously I can't speak for the whole art. This story is only talking about what was going on with me, in one particular situation. Maybe I'm not getting my idea across very well. What changed for me in this particular situation was I stopped the magical thinking, where my brilliant wit and obvious good intention would save the day and all would be well. Good would magically vanquish evil. Instead of wandering off into the fairy tale in my head, I stayed in the moment and was ready for whatever came. Most people may do that anyway. I had to learn that skill.

"What is disturbing is this unthinking attitude. You can have the best instructor in the world, but if you misinterpret what they're saying and doing, then the mistake is yours alone. A good example of this is the final statement.
Nobody trusts science, especially scientists.