Bingowings said:

Strictly speaking Dooku was as manipulated as the rest of the Jedi.

So really Obi-Wan should say something like, "We have all been deceived, even Dooku. Palpatine was behind everything, including the war. He is the Sith Lord we were looking for and now Anakin has become his apprentice."

I think that's vague. I mean, you could say that as the movie is already. I mean, Dooku was deceived. And he lost his head for it. The line really needs to somehow emphasize that Dooku was never evil.