I am sorry, I am confused with the problem you have of her word choice. He was being disruptive in class and she called him rude. He WAS being rude. The definition of rude is very broad, it can be as bad as offensive or as mild as ill mannered or impolite. And talking when they should be quiet, is impolite or rude.

No where in saying: You are being rude is she telling him he is a bad kid. An impolite kid, yes, a bad kid, no.

I would explain to your son what rude means and why she felt he was being rude and use it as a learning experience and let it go.