Let me tell you why. Memories you hold dear whether they're good or bad, stains you till the end of your life. Remembering how hard you tried from your first life or when they suddenly change when you just changed like they ask for forgiveness from what they did. It's too late they should've said nor tried to be better before it even happens. That's why she can forgive him but she can't stay with him.
Isn't just the book?? and oh please the fl was kinda dumb when she expects the emperors when while growing up she please him and do the daughter job and the emperor actually loves her unlike her real dad that abandoned her and living in the palace was kinda awkward though so maybe she should just run away.
She can't run away because she is literally now the fake princess. She will be captured and killed. Also she has no street skill. She only can choose from the both worst and she chose one for now I guess
She experienced how the emperor hated her as long as she can remember until the age of 9 when she started to change because of the book. The emperor do love her now but that won't heal the trauma she experienced at such a young age. So no matter how the emperor say that he loves her like daughter she still thinks that it was only because of all the calculated things she did to gain the emperor's favor. And a parental affection isn't supposed to be like that. It should be something that is natural like innate emotions and not a result of her trying to gain favors. And she knows that. That's why she was disappointed and hurt when she realized that Katherine doesn't feel that way. And with regards to Liguin/luguin/logan (I'll just refer to him as Mage Master) it is a different thing. Because the mage master's nature has always been like that. It's difficult for him to understand or be empathize with other people. Not because he is evil or what. It's just how he is. He also didn't abandoned her. Can't you see he's also trying and that he really do care about philomel just like his sons do to phil.
why did she pick the real dad when the emperor now really loves her like a daughter.