Head Coach is the one who decides who gets the scholarship, so IMO it should be he who sits with the player to tell him why he is not playing and how they will work with him to get the opportunity to play next year.
I would be leary of any HC who doesn't have the guts to do his job, and this is part of his job. Don't care how big or small the program is. It's obvious he didn't want to be the one to do it. The strength and conditioning coach is just what he is, the strength and conditioning coach, his job is to see that the player properly develops physically so that he remains free from injury.
And obviously, the die is already cast but I would suggest your son go back to the coach he directly reports to (hitting coach, pitching coach) if he has any questions, not you.