Her decapitation of others and imprisoning Osma were more horrific and arguably more heinous than what her boss did or intended to do, and unlike him, she had no redeeming qualities or sympathetic motives - she just wanted total power over Oz.
I don't recall any evidence in the film that the heads are still conscious, they just stare blankly, and as for the comparison to the Nome King, he turns everybody in the Emerald City except the Scarecrow to stone and he's the one that gave Mombi the power to collect heads in exchange for getting rid of Ozma, meaning he's directly responsible for most of her crimes. The only argument against him is he shows sympathy for Dorothy at one point, but it's debatable how genuine said sympathy is considering he threatens to throw her and her friends into a furnace for getting upset about him not telling him the rules of his game, a game he only let them play because he thought they had no chance of winning, seeing how when Dorothy wins he turns into a giant monster and tries to eat everybody alive. And don't forget the Nome King's Kansas counterpart Doctor Worley, he performs horrific experiments on his patients and locks some of them in the cellar after "damaging" them, and it's hinted that he might be more than just a counterpart to the Nome King when he says he plans to become completely human.
They all cry out Dorothy's name at some point, remember? That's what alerts Mombi to her presence. And aside from the degree of pity he shows Dorothy at one point, the Nome King's desire to be human and not confined to his mountain is somewhat sympathetic in of itself, as is his perspective that Emerald City stole what rightfully belonged to him. Doctor Worley might be arguably count though, since he lacked those redeeming features. There was nothing to indicate he and Nome King were exactly the same.
The impression I got is the consciousness the heads have while they're stored in cabinets is basically an extension of Mombi, seeing how they go to sleep at the same time as her, and Mombi's original head was the first one to shout Dorothy's name.
That means Mombi replaced the consciousness of the heads belonging to different individual women with her own by use of dark magic - like she shut off the other womens' very souls. That still sounds pretty effed up to me.
What I was saying is the Nome King gave her that power so he's just as guilty, and he has other crimes under his belt so he's technically worse, and considering he doesn't count due having some sympathetic qualities that should extend to Mombi as well. Compare with Greevil and Ardos, the main reason Ardos isn't considered a CM is because his father is ultimately redeemed despite being more heinous.
The difference is that Greevil raised Ardos and Ardos worked directly FOR him. Mombi is evil with or without Nome King around and worked WITH him. Nome King might have given Mombi her power, but what she did with it was her own choice, and the nature of her crimes is a good deal more horrific than even Nome King's.