Life isn’t always fair. I have lost count of the times I have seen a superior candidate for a position passed over or times a person is rejected by an institution that is inferior to others ones that offer a spot. Best not to dwell on it and move on.
Your son should have options with those credentials that 99% of people would rate better than BYU....Duke, Georgetown, Notre Dame...or even Emory or GT in Atlanta. I understand that there are a intangibles and legacy there that would have made BYU special, but he can start a new legacy with his own memories elsewhere. Take some summer religion classes at BYU and it’s all good.