So I'm wondering if shutting down their transfer capabilities after their 3rd offense is too late.
Your trainer (or his or her materials) was expressing an opinion about how far your bank should go in terms of flexibility. The outer marker he or she sets is a mile beyond the one I would have set; e.g. I would simply remove the interest bearing feature after the second offense in a rolling 12 month period. My second notice would say, "It's done; the disclosure for your non interest bearing DDA is enclosed." I'm not inclined to fool with people over trivia and that inclination has fallen with interest rates.
In essence, the "rule" is that you have a mechanism for putting a stop to it, not that you do it after X number of instances.