The fry carts are all still there and where they were before. The confusion comes in with the one change at Animal Kingdom where the Restaurantosarus went to serving Disney nuggets and not McDonald's nuggets. But there is still a fry cart there, and one in Magic Kingdom, and one in the Studios, and one at Epcot. All of them are usually lined up with families who are trying to get the kids to eat something they are familiar with.
Disney and McDonald's did sever ties at the regular restaurants with putting the toys into the Happy Meals. So McDonald's is losing out on a ton of money with Wall-E right now. But I really don't know if any other fast food place has picked up the exclusive contract with Disney.