Their reasoning might be not stupid: the problem might be not an "apple per day" the kid was eating, but the "special needs" kid himself. They might be forced (by some company policy or something) to hire him, but were lacking any means to fire him. And the kid might have been a bad worker. So they just waited until they had some "case" to legally dismiss the problematic worker.
Details are not present in the article, which is clearly written in a "poor kid, cruel corporation" mood.