Ah yes, good point. I forgot about Gunray's god awful line about not signing anything until her head is on his desk.
In any case, there are too many lapses in logic conflicting with goals for any of this to make sense. As Red Letter Media says, it comes across as a script written by an eight year old.
Anyway, it's all a moot point. Dooku will not be a Sith in my edit, nor will any members of the seperatists be responsible for the attempts on Amidala's life. Althought the republic and the Jedi don't see it this way.