I am guessing you can, but not 100% sure. I've heard that in certain places you can skip the side that comes with the meal (fries at stage door for example) and disney charges you less than the full price to compensate. I've heard of this several places, so I would wager a guess that they may do it with kid's food, but I am not sure.
This actually came up as one day I was really craving the mozzarella sticks from stage door, but didn't want the fries as I was just looking for a snack (and two fried foods would have been too much). The very helpful cashier rang me up and I was happy to see that I could sub for apple slices or have no side at all and it came up less than the regular price (I honestly can't remember how much, but it seemed the right amount for a side of fries). The CM explained that they do this all the time at most food places.