Disney previously tried to set up a system using bar codes on the mugs. It was tested at Typhoon Lagoon for day visitors, and the drink stations were out of service more often than not. There was a lot of complaining because guests had to go to snack counters or restaurants for refills, rather than using what were supposed to be conveniently located refill stations. Cast members would not be notified when drink stations weren't working, and problems ensued when they told guests to use one of the drink stations. I don't think that system lasted more than 3 months.
They will figure out a way to limit the all you can drink mugs to length of stay only. They just need to find a reliable and hassle free system. KTTW cards, while a good option, would not work, as you would most likely need to have the necessary card use the station. Most families would not give KTTW cards to small children, and the drink runner most likely wouldn't have everyone's KTTW card with them. Too many variables, and Disney would find they would have to devote one or two CM's just to help with the drink station.