Granted that Dooku was a "known enemy", but that alone doesn't screw up the plans. Since the clones can take out the regular Jedi and council members, it really comes down to Palpy eliminating Yoda, Obi-Wan, and Windu. I agree that the droid armies might have killed Obi-Wan on Naboo because the power station wouldn't have been destroyed. He couldn't defeat 2 Droidekas, even during AoTC, so he probably would have died. If not, Dooku could assassinate him outright on Geonosis. A Dooku/Grievous combo would destroy Windu, so even without Anakin, it would be possible for Palpy to take control. Anakin may have caused some confusion in the council, but it wasn't crucial to Palpy's plan the way the creation of the Clone Army was.