At first, it seems like it, but then I started thinking about it from an unbiased perspective.
Copy X is only protecting the humans, in his own way. The Reploid mass murder argument falls flat when you realize that Reploids are merely robots; sentient (for the most part) robots, but only robots. From what the people in MMZ4 said, they had a great life under Copy X; his death and Weil's takeover was probably the worst thing that could have happened to them. As far as they know, Zero's as bad as Weil.
No bias is fair, no compassion is ruthless, and the line between them is exceedingly thin.
Copy X's own position clashes with his policy, a robot labeling robots as inferior citizens, which in itself makes you wonder about his rationale. Though he himself is devoid of fear in his line of thinking, his actions manipulate the fear of others to rally them to his cause. A cause justified by labeling others as "sub-human" and handing out senseless accusations to excuse their destruction in a time of crisis.
Reminds me of Hitler.
Just because someone is charismatic doesn't mean they're not evil. In fact such people are considerably more dangerous than a non-charismatic evil person could hope to be. Atrocities such as this are justified by demeaning the victim, and that's the giveaway. They think for themselves, they're part of society, but they're not human, so it's okay. They're the inferior race, and the superior race is justified in whatever they decide to do with them.
For exactly this reason, I hold Copy X as not only evil, but the most
evil villain the MegaMan saga has ever seen. Because it's not just what he can destroy or what he can rule, it's his potential to corrupt the masses, to sway good people to the point that they honestly believe in the wrong side. Thus we have the Big Four.