Let the doctor take the crap out. They don't function properly, and are making him miserable. Why do you want him to suffer?

My mom had her tonsils out at ten. Before that she was never healthy a day in her short life, afterwards, never sick a day in her life. She's never sick. I have crap tonsils and have already had my adenoids out. I am always sick. Do what the doctor says, they know what they're talking about. Someday, your son might have an anaphlactyc reaction and his throat will swell shut. Without tonsils, it can't happen. I dearly wish I had my tonsils out. I almost choked to death earlier this year, when my throat closed up.

People with allergies have screwed up systems that treat the body as the enemy, it's not normal, and your can't see his tonsils job as normal. His tonsils are making him sick, not protecting his immune system.