Quote Originally Posted by Errorname View Post
Palpatine has, at this point, almost complete control over the republic and embedded the Jedi within a massive army that he can turn against them with a single phrase. He has positioned it so that when the Jedi do act against him, he can counterattack with the full force of the new Empire. Even if Anakin sides with Mace, the Jedi will still be outlaws, Order 66 will still be put into place, there will still be an Empire. The win-state for the Jedi Order at this point is not "save the republic", it is "stay alive".
Order 66 has not been given yet. If Anakin sides with Mace, Palpatine is dead. Dooku is dead. Grievous is dead. Now, there's a lot of political problems, depending on what the Jedi can prove about their motivations and actions, but I don't think there's any chance of the Jedi being genocided or outlawed. Worst case is Windu and Anakin get tossed to the wolves for political reasons.