Many WDW restaurants offer a sugar free dessert or fresh fruit.
Ask for sauce on the side.
Sub for brown rice or extra vegetables when possible.
Most counter service locations have a salad option.
Let the hostess know you have food restrictions and the chef will be able to make you something special, if they are unable to accommodate you on the TS menu.
Do you homework prior to your trip here:
http://www.wdwinfo.com/wdwinfo/dining/disneydining.cfm