>>2332399Madoka is not chasing her but she does want to be with her. That was the big part of her happiness in Rebellion, just being able to live happily with Homura. Madoka would also let Homura do what she did if Homura explained her goals beforehand. Her cause is noble, but her methods are self-destructive and Madoka would rather get torn in two than let Homura destroy herself. She would want to help instead of getting imprisoned, and explain that if she could be with Homura and see her happy everything else would be fine.
Her despair showed her true feelings about herself, she has no self-esteem and considers herself not worth anyone's attention. This is exaggerated by her devil persona, antagonizing the people she wants to be happy because her actions reinforced her ideas that she's the absolute lowest form of life in the universe, next to the Incubators. I still think Madoka can convince her she is wrong and make her heart turn colorful once again.