The question of what's harmful is separate from that of what's true. I'm saying here that science undermines theism (as in the intuitive belief that a person created the universe of natural things), regardless of whether theism is beneficial or harmful.
But as for the harms, I think theism itself has both benefits and downsides, like any other complex social phenomenon. And because the theistic intuitions and fallacies are built into us, they can be politically exploited, so the religious institutions and social hierarchies, too, are harmful as well as perhaps beneficial in certain ways.