You can ask to speak to a chef when you're seated. The chef will come out and go over your options with you. You can note the allergy on your reservation ahead of time, or notify Disney Special Diets (sorry, I've never done that so I don't have their contact info), or you can just speak to the chef when you get there. They will for sure provide safe food for your daughter.
That being said, if the citrus chicken is the only thing on the menu at Whispering Canyon that is appealing and you're going there just for that, I would try calling the restaurant directly ahead of time to see if it's going to work for your daughter or not.