My 2 year old has celiacs so I know what you are dealing with. I had no idea MSB even had GF options (they didn't last time we went). There is a babycakes in Downtown Disney, and they sell some of there stuff in a few spots (Beach Clubs dining hall for one). We find it easier to just breakfast in the room and pack lunches for her as the table service places are much easier to get confirmed GF meals than the quick service to me.
You may want to ask over on the DISabilities board. They've been very helpful with our planning.
Good luck!