So I agree, I don't see why thinking machines are a worse alignment problem than enhanced humans. See also the Wrath of Khan.
I try not to think too deeply about it, or I won't enjoy the story. How could a society have gravity suspensors, "shields", and lasguns, but no advanced computing capability somewhere? And why use swords/knives for fighting, when projectile weapons are so much more deadly? I still love the books, but I have friends who can't enjoy the Dune world due to its many contradictions.
Edit: I realize that "shields" supposedly made ordinary projectile weapons ineffective - but they had advanced drone technology (e.g. the assassin drone used against Paul, which was also stupid)