A.J.
Its safe and I'm in the situation! My daughter is 3 and has 2 cavities and will be going through the same thing. It is a genetic thing; my daughter brushes 2 times a day and has little princess flossers she uses at least twice a week. I had cavities at her age and so did my husband. Another thing to think about is baby teeth are naturally weaker teeth; they're made to go only so long and wear away and fall out so don't beat yourself up over this. You should look into a flouride rinse for your son. My daughters dentist recommended ACT flouride rinse for kids. She said if your child isn't great with rinsing and spitting, just dip a toothbrush in the rinse and brush it onto their teeth. Its bright pink and bubblegum flavor, my daughter loves it.
The procedure is very safe, I had it myself when I was 3. I hope this was helpful!