I just had a thought.
Remember when Homura crushed the doll that killed Charlotte and how some people thought that the doll was the Witch's true body?
Hear me out on this:
There is the theory that Charlotte's mother was dying of cancer, and Charlotte used her wish for a cheesecake to share with her mother. But she ate it all, and when her mother died, she realized that she could have used her wish to save her mom, thus resulting in her Witchification.
That doll that Homura stepped on may actually represent Charlotte's mother, and there may have been a bond between the Witch and the doll. This 'bond' represents the relationship Charlotte had with her mother while she was in the hospital and may represent the hope that they could spend their time eating sweets together if she had survived the surgery. And when you recall the theory that Charlotte wished for cheesecake to share with her dying mother but it all for herself, it makes more sense, as cheese symbolizes her mother. This would explain why when the doll was crushed, Charlotte died. Because when her mother dies, she realized she could have used her wished to rescue her mom. So when the doll died, so did Charlotte.
As for Charlotte's second form, that represents the cancer her mother had, and I suppose it could also represent Charlotte's selfishness: a sweet girl on the outside, but selfish and gluttonous on the inside. It's regeneration can also symbolize the power of cancer, and her first form doesn't fight to show her helplessness against the cancer
Does any of this make sense?