I don't know why you would be against intentionally throwing inside. The inside line is legally given to the hitter. But that, in no way, should discourage a pitcher from throwing inside any more than if the hitter were standing as far away from the plate as possible.
Throwing inside is part of the game. If a player is aggressive enough to stand on top of the plate to take part of what is the pitcher's, the pitcher has a right to be aggressive as well.
Your boy needs to say something. There is nothing wrong with respectfully pleading a case. His pitcher needs the support. If things are technically legal, then you have to work with the situation. But, by all means, don't back down or give in. If you give a kid three free bases, you've at least made him earn them.