Anakin Skywalker didn't kill Count Dooku instead he captured him and with his help took down Senator Palpatine.
By the attempt to capture Palpatine Anakin was injured by the Senators Force Lightning so he had to be put in his suit.
Now the Republik and Separatist Federation were joined in an Empire under the control of Senator Amidala, Organa, Dooku and Bonteri.
There are also a few Force users in the lower ranks of the Goverment (White Jedi, Grey Jedi, Black Jedi).