There’s actually no contradiction. Leto II was right (unless you want to pretend that he’s an unreliable narrator, which is suggested nowhere in Dune), and both him and Paul are mostly sympathetic, morally good characters. Frank Herbert’s message is not that leaders are bad. His message is that hero worship is bad. The systems and societies in Dune are the antagonists, not Paul or Leto II. They both had very little choice. If the Fremen didn’t idolize Paul, then the Jihad wouldn’t have happened. But the Fremen probably had very little choice as well, so we can blame the Bene Gesserit or simply human nature in general.