He's not even supposed to be able to throw a pitch in 2016, is he? The commitment is to keep him on the 40 until ST is over and he can be moved to the 60-Day, during which time you are committing your financial, medical, coaching and training resources to his rehab. And then, having done so, you have to keep him on the 40 prior to next year's Rule V (though not protecting him probably a reasonable gamble).
I imagine he will clear this time, and the Pirates are hoping he will. Whereas the Phillies were ready to move on, for the sake of both sides, and they and the Pirates were able to do each other a favor roster-wise at the time.