Welcome aboard, Sarah! You must be so excited to set sail this fall on your very first Disney cruise! Let me reassure you that Disney Cruise Line is excellent about accommodating guests with food allergies.
Be sure to note your allergy information on your cruise reservation if you haven't already. Disney Cruise Line does suggest that guests with food allergies try to eat most, if not all, of their meals in the main dining restaurants, as the kitchens and Cast Members there are better equipped to deal with food allergies. The galleys in these kitchens are much larger, assuring cross contamination of allergens is not an issue. So, when at all possible, plan to dine in those restaurants. Since your same dinner servers will be with you each night, you won't have to re-explain your food allergy each time, and they'll be aware of giving you suggestions for alternatives. You might ask them each night which restaurant they'll be working in for breakfast and lunch the next day so you can sit at one of their tables for those meals too!
If you'd like to dine at Cabanas buffet or the quick service spots near the pool deck, you'll need to be more careful with what you choose. You can always ask the Cast Members there to verify any choices you make, and if they don't know, they can find out for you. You may even chat with your servers in the main restaurants to see what they suggest as far as options on the pool deck too. I do believe that
Luigi's Pizza near Donald's pool offers a gluten free pizza crust. Check once you're onboard to be sure it's still available.
One thing is for sure, Sarah: You are in for a fabulous cruise and the servers and chefs are there to ensure that even with a gluten allergy, you will still enjoy delicious food and wonderful service.
Have fun planning!