Blue Buyao (sp) has a few meat dishes that should be atkins friendly, the side dishes might not be, but they should be able to subistute a green salad in stead of potatoes and such.
White water snacks (near the pool of the GC) has egg dishes in the morning. Should be able to get eggs, bacon, sausage...I've heard wonderful things about the Prime Rib at Storytellers Cafe (also in the GC) "can cut it with a fork" type of things.
Bengal BBQ near the Jungle Cruise had chicken and beef skewers that are wonderful. They may be marinated in a sugar base terrikki, but I'm not sure how much of that really matters. They also have a great grilled veggis skewer. I know the potato would be out of his diet, but it had zuccini, squash, tomato, and green pepper.
Plaza Inn has a 3 piece fried chicken dinner that comes with mashed potatoes, green beans and a roll. You might get yourself a kids meal and a side salad (the kids meal is quite large for 4.99 and the side salad is about 3.00) then give him the side salad and take his high carb sides.
Any of the buffets will have plenty of high protein foods, but I'm not sure if you want to do character meals. Goofy's is always character buffet, but the buffet at Storytellers is only characters in the AM and even at that the characters stay outside in the lobby.
If you check out
www.colddeadfish.net , Cindy does wonderful menu's and reviews of the places to eat around DLR. There is also a few places outside the resort near the hotels on Harbor that would be a quick 5-10 minute walk. Tony Roma's, Mimi's, McDonalds....a few others but I can't remember right now.
You could always just get a burger (without the fries and just take off the bun) as a last resort.