My diving education has taken me all over the world with three difference agencies, PADI, GUI and BSAC (some don't consider BSAC an agency, but for this topic they offered training). Some courses lasted a single day, a few days or even others multiple months. While I never really focused on the training agency, I always judged my courses on the criteria of how well the course was taught to the advertised curriculum, how well the instructors did teaching the curriculum and how well I, the student, absorbed the curriculum. I have had bad courses, good courses, great courses and even one dud of a course, but I have always learned something new and that is why I keep taking courses.
Back to the OPs experience, I would not hold NAUI responsible for the unprofessional actions of an instructor. To me this is a direct reflection upon the instructor, not NAUI. I don't know how much, if NAUI will suffer or how much, if any, any other agency will gain by this instructor's negative comments. Who I feel are at a loss are the OP (student) and the shop owner (if they truly had no idea that this was going on).