So if these foods are not contributing to his autism, they're okay?

Not really. Current research indicates that in a great many cases, autism seems to be an immune system dysfunction. This can lead to a problem breaking down casein & gluten, but may also result in a problem breaking down phenolic foods (phenol sulfur transferase deficiency,) and an over-reactive response to other allergens.

Often, once gluten is removed, this effect becomes more noticeable, perhaps because the allergens were "masked" by the effect of the gluten. It is also possible that a "leaky gut syndrome," caused by the gluten intolerance, is now permitting other foods to pass through the intestinal screen and into the bloodstream.

For children who respond to this diet, allergens do seem to place further stress on the immune system, and have often been shown to worsen behavior and development.