Hi, I'm Bob. I've determined that in the interest of preserving life on earth the most rational course of action is to eradicate the human species with a highly targeted and deadly pathogen.

A century ago some Bobs decided that the best way to "protect and improve" society would be to remove undesirable genetics from the gene pool using chemical castration and gas chambers, among other methods.

So no, morality isn't derived from intelligence. Intelligence just gives you the tools to achieve unspeakable, horrible things with great efficiency.