Perhaps new quarantine protocols can achieve the desired ends. Since there do seem to be temperature tolerant strains among carrier fish simply warming new arrivals in a qtank and waiting to see if they die isn't going to cut the mustard. Using several uninfected "canary koi" in a prolonged quarantine cycle would help prevent introducing infected carriers if that protocol is strictly and verifiably enforced. Ungraded fry swapping could still take place if a similarly strict quarantine methodology is utilized but it would be a considerable added expense for ungraded fry.
Perhaps the prefecture could establish a central "quarantine co-op" through which all exchanges could be processed. In that manner the operating expense could be shared and minimized while providing a central point of control and disease prevention. It would also make a strong statement to the world that the prefecture is seriously addressing the issue in an effective manner.
The issue that may be irreconcileable is summering customer Koi. The high cost of such a strict quarantine method could make it unaffordable for all but a handful of wealthy show fanatics.
Your point about the long term cost to the hobby is key. The tradition of exchange has made many improvements possible and if a safe, reliable way to keep that advantage cannot be found future refinements will be delayed by decades.