Dooku's agenda was Palpatine's but whereas Palpatine did it for himself, Dooku wanted the Empire for the benefit of the people. He saw, as many right-thinking persons do, the total failure in democratic systems; the endless corruption where the government continuously fails to meet the needs of the people...despite being "run" by the people.He believed that under a single ruler, this could be remedied. A benevolent despot who would act and that action would result in reaction, kinda the opposite of what the Old Republic did.
I'm wondering how you are coming to the conclusion that Dooku even had the best interests of the "people?" If he even had any hint of morals, he would not resort to arsony, blackmail, or brute military force to get what he wanted. What more, why would he resort to biological weaponry and bombing civilian sites in order to defeat those star systems siding with the Republic? It seems he had a pretty good idea that what he was doing would cause more suffering, not prevent a greater evil from continuing.
There are numerous sources highliting Dooku's depravity. In the ROTS novel for example:
"In fact, he has never been entirely sure what beings mean
when they speak of friendship. Love, hate, joy, anger-even when he can feel the energy of these emotions in others, they translate in his perception to other kinds of feelings. The kinds that make sense.
Jealousy he understands, and possessiveness: he is fierce when any being encroaches on what is rightfully his.
Intolerance....
Spite is a recreation: he takes considerable pleasure from the suffering of his enemies.
Pride is a virtue in an aristocrat, and indignation his inalienable right: when any dare to impugn his integrity, his honor, or his rightful place atop the natural hierarchy of authority."
It highlights that human emotions are alien to him; concepts such as love or joy. Jealousy, intolerance, spite, and pride are what he understands. He believes himself to be superiour to any other being, and that his abilities and powers give him rights over lesser beings. If he were "morally grey" then he would possess at least some redeeming qualities, such as the intentional well being of those he rules.
These emotions seem to imply that Dooku never really had the interests of the Confederacy or the allying nations in mind; he wanted power, as all sith do. He was hiding behind the facade of the Confederacy to gain that power, to seem appealing before the public eye.
Also, for him to believe that a democratic system is corrupt and a totalitarian government ruled by himself and Sidious is not, well, that seems to me another sign of his pride, nothing more.
Finally, someone who subscribes to the theory that hatred is of paramount importance in someone's life seems to be the living definition of evil.