It won't be a problem. All you are asking them to do is take one normal item off and add another normal item to it. So instead of maybe getting one French toast and two pancakes that are normally served, you'd get no French toast and three pancakes (or whatever). That's probably the easiest substitute at a Disney restaurant.
The only thing they won't substitute for that breakfast is the Tonga Toast. I tried, and then got the tonga toast by itself. After seeing it, I can see why!