My mother special orders just about everything she eats, and did so at WDW -its no problem. Table service restaurants are better able to accommodate than counter because they just have more to work with. Just tell them exactly what you want, be as specific as possible, make sure you say its for health reasons, and they will make it for you. All the good table service restaurants will be fine, but I will list some places I found helpful:
I found that at AK, the ice-cream carts have a small non-fat ice-cream cup (the listing is small on the bottom of the menu).
The parks have lots of fresh fruit available as snacks.
At MK, plaza restaurant has nice salads and a veggie wrap. Just order exactly how you need it - no cheese, no dressing etc.
California Grill can prepare pretty much however you want it. My mom had sushi/cal roll (make sure no mayo or tempura).
For Breakfasts, you will do much better at a table service restaurant (order egg white omelettes dry or oatmeal made on water), unless your mom wants a bagel or something like that.
At Epcot, for dinner, the japanese restaurant in the front room, my mom got sushi (rolls) and salad (no dressing).
