I do wonder what a more permanent solution for these sorts of situations could be, as right now these things are case by case. Either Nintendo tolerates the use of cloned cartridge IDs (which is something no game company/publisher/whatever have you would ever accept), or they bring down the ban hammer on random people who just bought a used game and had no idea it was used for copying (which is just a dick move). Nobody buying a used game is going to have any real idea where it came from, and in a lot of used stores the carts probably get mixed around anyway. Having any sort of checker for cloned IDs would also be difficult, as Nintendo's systems probably only catch it when both are in use at the same time. Perhaps they could use some system to look for MIG Switch use specifically, and only block that cartridge? That would probably be the best way to go about it, but I'm not so sure about the technical details that would make such a thing work, as it would require some reverse engineering of the MIG Switch.

EDIT: I do think as well this article is too generous to Nintendo. The writer focuses on how easy it was to get unbanned, rather than the ban in the first place. Nintendo should at least start sending an email warning or something before deciding to block online. That would give people a change to figure out what is going on, instead of waking up one day to find they can't access the eShop or GameChat.