Just finished reading this and Botan is complete garbage, not because she got angry, not because she left but because she didn't come back. Everything could have been resolved but she was too selfish and drowning in resentment and bitterness for her sisters who she saw as having it better than her, she was a petty human being looking for a way out in the end.
I can understand her being angry at Kashiwa since he more than earned her anger with his holier than though attitude but Sakura and Momiji were worried about her being abused and didn't deserve to be abandoned again, any adult parental figure who abandons their child is absolute scum.
You saw the trauma with Momiji when she was worried that Sakura would leave her, she had seen parental after parental figure drop out of her life one by one since she was just a child and having to put her faith once again in another parental figure only a few years older than herself would make her entire life completely unstable.
Botan knew this and she didn't care, she cared more for a relationship that would inevitably have ended with her being a homewrecker or her being abandoned.