I asked my doctor if I had celiac disease instead of crohn's, he said no celiac, he said I have crohn's. When biopsies are done, they can tell it's crohn's patches. Apparently they can do a blood test for celiac, according to my friend.. I'm sure the doctor checked your son for celiac disease.
My friend has it, and lent me a book called Wheat Belly by William Davis. I just started reading it, and he explains that our wheat is not like our grandma's, today it is hybridized and chemically altered saying we are reacting to that.
I've only read a couple of chapters so far, so I'm not sold on a gluten free diet just yet. Will keep reading. If your son feels better on a gluten free diet, then he should continue to do what he's been doing.