My DD and I are both gluten free (and I'm dairy free). The mac and cheese is the only substitute I've found in the parks that is higher priced. The mac and cheese was at Liberty Inn, where they serve it frequently enough that it's programmed into the cash register. I had the same experience at the resort food courts though. Mac and cheese is considered an adult entree. That's in part because they only have one size of mac and cheese. It's a 9 or 10oz Amy's frozen mac and cheese and it comes with no side items at all. That is my one major complaint about gluten free foods in the parks.
As for regular counter service - you should really contact Brenda because you know your child's preferences better than I would. My child won't eat anything that's gluten free and on the children's menu besides carrot sticks, grapes, pudding and chocolate milk. When we have the dining plan she and I just split adult meals. When we don't have the dining plan I just expect to pay more out of pocket, and I buy her a lot of snack-foods.
You can pre-arrange CS meals (you order them in the morning and tell the manager when you'll come back) and you may be able to get a custom children's meal at a children's meal price that way, but I've never tried it. Apparently there are chicken nuggets/tenders and similar items available that way. I've never had enough faith that it would work well to try it. It's just hard to time your arrival with the prep of hot, fresh food.
As far as substitutes being available - they are available to varying degrees. GF buns are somewhat common now, and there are a few specific places you can get gluten free macaroni and cheese, pizza, gluten free cookies or brownies, etc. Some of it requires advance notice, none of it is ever guaranteed - but they do a fairly good job of keeping stock. Substitutes do take a long time, and you should be prepared for that. I ordered a GF mac and cheese and a GF hamburger at Liberty Inn. It took 15 minutes and that was very fast. My average wait for specialty substitutes was usually around 30 minutes. The resort food courts at least have buzzers so that you can go and sit until your food is ready.
I've had to send food back as many as 3 times before I got something that wasn't obviously contaminated - but that is the exception more than the rule, and it was at the end of what I'm sure was a very long day for the CMs involved.
You can ask for a mickey plate, and I've done that. Then I just move all the macaroni to the center of the plate and put the side items that I purchased separately in the ears and she's happy. It just helps to know that's what you need to do.
Another thing to be aware of is that the lists of GF items Brenda sends out are not all-encompassing. They are usually entree only, and you'll need to check ingredients for side dishes at a CS location.
Honestly, I've had very, very mixed experiences with gluten free meals at WDW. They do a great job, and they try really hard, but it makes things a lot easier if you stay as alert as you would anywhere else.
Thanks!!
