Hedenberg,
If a HS baseball coach is not aware of the many great sidearm pitchers in baseball history, and what they can do for a pitching staff, he may not be willing to give you the chances that you need to develop yourself further within his program. It sounds as though your motivation to condition and train for pitching might really need to come totally from within yourself, because your head coach may not give you much encouragement, or at least he may not take the time to develop your personal style.
It's probably never a great idea to openly defy your head coach. If you feel strongly that you're on the right track, in spite of your coach's mandate to "throw from over the top, or else sit", maybe you can give the appearance of agreement with him more than you actually do agree.
He may have valuable knowledge to impart to you, despite an apparent ignorance of sidearm pitching in baseball....perhaps you both will find common ground on some of the things he knows well.
Baseball is results-driven in most HS-level programs, so if you are eventually able to demonstrate that your pitching style could be an asset to the team, you will hopefully get some chances to prove it in games.
In a situation like yours, your own attitude will mean a lot....if you grumble and whine, that's a road to sitting on the bench and/or being cut from the team. If you keep a positive attitude and stay focused on developing into the best pitcher you can be, your life in HS baseball may go in the direction you want it to.