Some of the injuries to pitchers happen because of the ignorance of pitch counts.
Our high school coach had my son throw 125 pitches and 140 pitches in two separate games. Supposedly this coach was a pitcher in a small college during his younger days.
Now compound this with kids playing in the field after pitching or pitching in one game and catching in the next.
I think as parents we need to make a hard stand about this. It's not easy being the bad guy especially with larger schools who have more kids to choose from.
Its on you, why did you allow it?
Thats the issue maybe, parents are afraid if they say something their son will not be in the game. Your son is being used that way because he is good.
Protect your pitcher.
My son was a freshman on Varsity last year. The first game my son pitched a complete game that gave the other team their first regular season loss in 2 years. So pitching 130 pitches was easy to forget. lol
The second time is when I learned that the coach really didn't care about pitch count.
Armed with this knowledge I need to talk to the coach and ask him to enforce a pitch count for my son. Either that or I can work out a signal for my son so he knows to claim to the coach that his arm is tired. 
Now throw in the fact that my son was the starting Varsity QB this year and now his arm health should be protected even more.
So what I get from your post is that...
1. Winning is more important than your son's health
2. You're OK with turning your son into a liar instead of teaching him to stick up for himself and talk to adults
Come on dude your first point about him beating a great team is exactly what TPM is talking about. What if he has pitches his team to that win and then next time out blows out his UCL? Was that win worth him having surgery and being set back at least one year?