Just my two cents. I switched to a minimal shoe for my daily training, and the pounded led to herniated discs in my lower neck and upper back. When I went to a physical therapist to work on fixing my back she said she sees more runners now (a sports-based physical therapy office) than she had in the previous 20 years. And almost every single one has come in with minimalist shoes.
Her advice was essentially, If you want to run fast over a short distance (less than 2 miles) or slow over a long distance (slower than 12 minutes/mile) then minimalist shoes are the way to go. Everyone else needs to get their stride analyzed and to wear appropriate shoes.
Since this is your son's first year, I doubt the coach had him above 35 miles per week. So he was probably fine in his frees since he wasn't running a ridiculous amount (and he is likely a fairly light-weight efficient runner anyways). But I would still suggest getting his stride analyzed -- Who knows, the shop might say he should stay in minimalist shoes.