That was my initial theory, but it seems as if Barriss is self-motivated. For her, Dooku could represent all that's detrimental about the Jedi Order. He's a former hardline Jedi, now a hardline Sith. If Barriss is so intent on punishing the Jedi for "serving the Dark Side", then why would she align herself with the one confirmed, out-and-proud Sith in the Galaxy? Certainly, a new apprentice could give Dooku a chance in the intra-Sith rivalry now that Ventress and Savage are gone, but it's harder to imagine Barriss being that apprentice than her serving in other capacities. Palpatine, meanwhile, can take on different personas for different people. As Chancellor, he could present to Barriss a facade of being a reluctant leader, pressed into accruing more power by the likes of the corrupt Jedi Order and the Senate militarists. The rumours of the existence of "Darth Sidious" don't appear to be taken seriously by the Jedi beyond the Council due to the apparent existence of a Sith duo in Dooku and whatever apprentice he takes on, and many Jedi probably have never even heard of Sidious. Barriss, with a commuted death sentence, could be gradually brought under more and more influence by Sidious through whatever persona he chooses. Well, I suppose Barriss the Dark Acolyte and new apprentice of Darth Tyrannus would be preferable to dead Barriss.