Shadow Weaver is more evil than Hordak in almost every way. She was the one who conducted the abuse, along with other high-ranking Horde members. He mainly stayed in his lab while SW, and later Catra, planned to destroy innocents. Not to say it wasn't his fault, though - he intentionally created a machine of conquest that destroyed thousands of innocent lives.

But what so many people fail to realize is that Hordak was literally made to fight. Shadow Weaver and Catra were perfectly aware there was a moral compass, but chose to ignore it anyway. Hordak wasn't. There was never any good and evil for him, just the will of Prime. Meeting Entrapta was the first time he actually realized there was a life beyond Prime. And then it was taken away from him.

So yeah, I think that when he realizes Prime is just a selfish asshole who never cared for him, Hordak, with the guidance of Entrapta, perhsps, would do the right thing.