It is all a massive con job, GL has done it before, if you are old enough to remember the trailers and posters for ROTJ. All you see is luke in black standing side by side with vader. This gives you the impression he has turned.
The whole point of the sith is to trick people into thinking things that are not true, they rule by manipulation not by attacking. Palpatine is the greatest manipulator of people i have seen, if the prequels do anything they have proven that Palpatine is the puppet master of the galaxy.
He gets Dooku to say 'join me to destroy the sith' or whatever he says to Obi1 in order for Obi1 to think that he has the interests of the republic at heart rather than his masters. If ob1 thought that dooku was a sith lord on his masters orders creating clone armies it would make it obvious that the chancellor was the sith master when the chancellor keeps pushing for their use. Palpatine is pushing for clones a lot i think in this one and he uses his apprentice to give the senate reason enough to grant him speacial powers. Remember Dooku is the leader of the separatsits mentioned in the tralier. It is the old start a fire and put it out yourself routine to make yourself seem the hero or to to break down democracy just enough to get the use of emergency powers ( i think GL reads his 1930's german history books ). The irony of this one is that he uses the threat of his creation to further gain power in the senate. I think people missed the beauty of that in TPM. oh well.
Bye the way - i have the feeling that Yoda knows who the Sith Master is when he says 'begun the clone war has'. He knows that the jedi are now the outcasts in the republic and that they will have to fight the clones to save themselves against the new order.
wait and see. GL has been setting this one up with an eye to history.