The paper cups have also had chips in them for quite some time. They have been set to allow three refills within a set time period, I believe two hours. If Disney had wanted the policy to be "no refills," they could have easily set that in the chip. I have never heard of that being the policy.
Also, it does totally make sense to offer both. Refillable mugs are sold as a benefit over single serve drinks because you pay once for them and then are able to use them for the entire length of your stay. If you're there for ten days, you can use them for ten days. Someone could get 50 refills in that time and be covered. With the paper cups, you're buying a beverage for one specific meal and, at maximum, are limited to two hours in which to get your three refills. Not to mention that your mugs go home with you. I use ours for coffee every morning on the way to work.
The paper cups are hardly a substitute for the refillable mugs.