MODOK falls apart because she can't manage it. Her plan to fight the aliens involved risking innocent people, and that's what made Vince turn against her and the team.
She pissed off Miles because she thought killing one of his classmates would help him. Then she turned on him for objecting, and got her ass handed to her, and arrested. She was busted out, sure. But she ruined her chance to impress someone she really cared about.
A lot of people (including her heroes) dislike her, and she had to learn a lesson. She gets called out on her behavior. each, Cecil comes back. But he's not happy as a ghost, and she goes on to get another body for him.
The whole point is that she fucks up and learns from it. Like honesty, what are you expecting? That she gets her arm cut off? That all her friends agree to murder her in her sleep?