I think you might have the best luck if you check out the Gluten-free threads. Also, if you really spend time and dig through the menus you might be surprised by what some of the CS have. While certainly not the greatest selection, there are options.
DD has lactose intolerance (very bad, as she can not even have butter as an ingredient) and I spent hours looking for dining options. I made a list of foods and restaurants to put in my iphone and we ended up having the most diverse CS meals in 3 years!
Here are a couple that come to mind
Epcot: (CS) Japan (grilled teriyaki chicken even in a kid meal) and The Sunshine Grill in The Land (rotisserie chicken, real mashed potatoes, veggie sandwiches, salads, soups)
DHS: probably the least options... we ended up at Pizza Planet (DS request) and got DD a soy cheese pizza (was actually good!) and we had salads and split the pizza. For TS in DHS Sci-Fi is a good option and the tofu dish there is pretty good.
MK: we ate at the taco place across from Pirates of the Caribbean. They had decent variety and a decent topping bar with lettuce, cheese, and tomatoes. You could also choose beans for the tacos and get rice mixed in with the beans.
A lot of the good food options are there, just not really on the menus. Sometimes you have to ask and wait a few minutes, but it is not too bad. Also, all of the CS restaurants have apple slices and carrots and grapes as options instead of fries.
Hope that helps.
