Hello Stella,
Maybe you have to make more mud pies for your son to eat instead ;) Actually, I wouldn't know what concentration of harmful chemicals have been found in wax, but basically you'd have to live on another planet to avoid contaminants completely. Even breathing is dangerous...but, everything in moderation. Your son might just have to limit his intake!
Anyway, I've heard plastic foundation without the wax coating isn't liked so well by the bees. The beek who has a hive here spreads his own wax coat on with a roller. That would be much the same for you as using foundationless wax. You might not avoid chemical contaminants completely, but they would be your contaminants. Or you could cook some meat and vegies for the poor boy :-D
Lone