Sounds like you just need to trust the professionals. It's for his safety and theirs.
Our dentist told us that kids cavities may be the result of sugar added drinks, too much juice, fruit snacks or any "gummy" candy, and simply not brushing well enough.
Make sure you help your child and "check" his brushing by re-doing it EVERY time. Use fluorinated water and toothpaste. Save "treats" for dessert, after dinner, so that he's brushing almost immediately after having them.
If they get junk food, sugary cereals, juices, sodas, candy or gummy vitamins in the morning or at lunch the sugar gets trapped in their teeth and sits there all day. The sticky foods "catch" other foods and give bacteria more to thrive off of, especially in their molars.
Ask your pediatric dentist if your son's teeth should be sealed. This is a quick brushing on of a solution that dries almost instantly and will help fill microscopic holes in the teeth to help prevent future decay. They should be able to do this while he's already in the chair for this next procedure.
Also, ask about his using mouthwash. The dentist may even recommend a professional strength one. Your son may be "mouth breathing" at night, causing dry mouth. If this is the case, the bacteria are not "washed away" by salivia during the night. Increasing his chances of decay. There is a mouthwash sold over the counter to help with this issue.
Best of luck - I hope this helps in some way.