Well, I don't know exactly what happened, so correct me if I'm wrong, but if people abused the arena system by refreshing it many times with Kobans in order to get a lot of XP/money rewards (although the XP gain from arena fights was pretty low, wasn't it?), I'm pretty sure the devs could have implemented a fix that would not have ruined the feature for every single person - 99% of which did not abuse that system !
For example :
1) Make the Arena Refresh price increase every time you use it - 24 Koban the first time, then 48, then 72, then 96, and so on. They could even make it increase even faster, doubling every time, to be more dissuasive : 24/48/96/192... And then, reset the price every day, of course.
2) Drop the XP/Money/item rewards from Arena fights ONLY if you just used Kobans to refresh the list. But you gain those XP/Money/Item rewards normally if the list was automatically refreshed after 30 minutes.
Unfortunately, the devs fixed an "exploit" in the laziest, fastest, most despicable way : By making the feature useless and not worthwhile for everyone, especially people who play normally. That sucks.