I'm with you. I thought that particular plot twist ruined the entire movie, if not the series. Imagine a much more tragic outcome: Dooku and his allies are fueled by their hatred of the tyrant Palpatine. The Jedi, in their arrogance, gather all their powers, and, in concert with the genocidal abomination that is the clone army, they crush Dooku and the rebellion. When in despair and horror they realize they have been manipulated by Palpatine and The Dark Side, there is no recourse: They have killed Dooku, the only one among their ranks who had the power and the integrity to challenge Palpatine, and they must flee in cowardice, as Skywalker hunts them down and mercilessly assassinates them.
I think you may have described a pretty good chunk of the plot that we'll see in Episode III, along with the Anakin Skywalker - to - Darth Vader transformation and the concealment of the Skywalker twins.
I don't necessarily think that the scene you refer to ruined the film or the overall story, but it does beg some questions, such as: How does Count Dooku know about Darth Sidious, but none of the members of the Jedi Council have been able to sniff that out - even *after* the Darth Maul incident? I know, I know... "Always in motion, the future is..."