My practice area isn't full-time family law, but I've handled a couple of cases where the child had medical needs. It's really important to have a confirmed diagnosis with doctor's instruction. If he doesn't comply with doctor's orders, then consult your attorney.
For some parents (on both sides of the fence), controlling a child's diet is perceived as an attempt by the other parent to extend "control" of the children into the reach of the other parent's parenting time.
Having gluten free diets becoming so popular is both a curse and a blessing. On one hand, there are a lot more companies getting into the gluten free market and there are more choices available. On the other hand, a lot of people think it's a fad and not a medical necessity.