There is always a choice. Sometimes you take the lesser of two evils. It seems like the coach was willing to make your son roll the dice with his short- and long-term health. That's a safety issue. One of the very, very few times a parent should and must intercede on behalf of his/her son. If this all happened real-time in front of everyone, that would be highly unfortunate.
I'd recommend not talking with HC one-on-one, or at the very least let the situation cool for a day or two. I'd recommend setting-up a conference meeting with the HS AD or principal in charge of sports, you, and the HC. Make sure you are heard, he has the opportunity as well, and the administrator knows the context and is in a situation to intervene if there is (unfair) retaliation.