Not that I am crazy about how Kelly handles any qb situation but Zaire never got the short end of the stick.
It would have been hard to justify say he had "outperformed" Golson going into 2014 especially given Golson's success in 2012. Kelly gave Zaire an opportunity at the end of 2014. He then seemingly beat out (or at the least kept himself in play for the #1 role) Golson in spring 2015 probably causing Golson to transfer. He then play 1.5 games, looked good against a bad team and look mediocre against a bad team and got hurt. He goes into spring and fall 2016 coming off injury and was apparently beat out by a superior qb (sorry Kizer is a superior qb to Zaire).
Zaire had little to gain in transferring going into fall 2016. I doubt he had much cache for any school to look at anyway, coming off a little more than 2 games of experience and a nasty ankle injury. He would have sit out 2016 and had the opportunity to play only in 2017 anyway which he still retains anyway. By staying, he gets his ND degree, something he clearly values and can play somewhere else next year if he chooses. The only way someone could opine he got 'screwed' would be based on what he was told by Kelly after the end of spring practice as to whether he was still in the running to start. We don't know what he was told.