Agree with joes87 here. My son is going into his junior year at a top D2 university. In two years, I have seen 3 players get cut primarily for attitude problems. In one case, the player felt he should be a two way guy and coach wanted him as a PO. He was a good pitcher and probably would have been a starter sophomore year. Kid debated with the coach during his exit interview and coach just told him to pack his stuff and go somewhere else. Another kid was a pretty good relief pitcher, but also felt he should be two way. He got cut at the end of the year because coach didn't think he was a good teammate because of his attitude towards not playing in the field. Third kid was a top weekend starter as a freshman and sophomore. Got in some off field trouble, did not have a good attitude and work ethic. Final straw was being late to a practice and coach cut him. Went to an NAIA the next two years and wound up drafted. Even the good players will not be tolerated if they do not have a good attitude.
As others have said, I don't know enough about all the details here, but your son should learn to deal with this situation without running away. It could crop up again in college and it will not be dealt with kindly.