Dooku didn't leave because the Jedi were wrong, per say. He left because he was seduced by the dark side of the Force and agreed with Palpatine's views for a new order. He was evil the minute he pledged himself to Palpatine's teachings and methods. Especially if he did kill Sifo-Dyas, a fellow Jedi Knight. To betray everything that you once believed in and side with evil by committing acts of evil, then you become evil.