I'm in a similiar sitation as the parent, As an American living in Japan, married to a Japanese national, Japan treats me with respect and courtesy with very little stress or hassle if any, at the airport.
Outside of the airport is another story. My wife though has not had any problems at immigration and we regularly enter at LAX. She also has a green card.
I'm surprised that they hassled his wife or asked how much money she had on her, wierd.
But this whole pre-registering thing is just plain stupid and other countries should do the same, so the stupid US government will drop this nonsense.