I will not claim it is intelligent. But, I also do not believe in language is made of intelligent design. Things evolve. Sometimes in clever ways. Sometimes in odd ways.
That said, most contronyms give absolutely no cognitive dissonance. That "to dust" something can mean to remove or to add something has rarely caused confusion. Only place I have ever seen it was in some old children's books, to be honest. Which is half the reason they are fun. Teaching kids contradictions is what keeps some of it interesting.