To be clear, Paul is not omniscient. He can not see everything. The book explicitly states that just as our eyes can not see beyond a mountain when you stand in a valley, prescient sight is also not absolute. He also can't see other prescient beings, like guild navigators.
Paul is a product of his environment. He believes he has a legitimate claim to the throne and he's willing to use the power of the Fremen to make that claim and destroy those that have betrayed him. In his mind, the Jihad is an unfortunate byproduct that he reluctantly accepts because any path that prevents the Jihad also prevents him from claiming the throne. This is why he's an anti-hero and not a villain. In a vacuum, his actions against those who betrayed him are justified, and those people are more traditional villains that deserve to be destroyed. But, he has prescience and knows the results will be catastrophic, thus he is not a hero.