Seen some spoilered speculation (but avoided reading too much as it is not entirely clear if it is real spoilers or not) about why the father did as he did. And overall it touches on the same thing I speculate: that the fathers flashback to an seemingly adult mc suggests he has knowledge of a future. So possibly reincarnated individual with knowledge of the plot, or regressed, or oracle, or simply strong memories to someone she reminds him of, that expect her to cause / associate her with, some calamity or injustice.
But considering his reaction to it, I really feel like the father has neither read frankenstein (tbf I havent either, but I have read tumblr threads on how it is an allegory on parenting, that he hasn't read either) nor heard of the concept that all humans are born innocent. Not realizing that however he raised her was the issue, lest plot-shenanigans or curses or the like was the cause. Because his response to whatever concerned him was absolutely objectively incorrect.
Also, if it is either tensei or oracle (not regression), then he also clearly have never heard of Oedipus's story (or rather, his father's).
From what I understand Magnolia was someone to be shunned and can do no right in his mind, he was taught through the actions of his parents that she was a third class citizen in their house, someone that's bellow even the cat.
For him it's like losing a fixture of the house something he always thought will be there, perhaps an example to be avoided.
You put it really well. The kid was a brat, sure. But he was never truly treating her
poorly. Rather, he were treating her as he had been taught to, but still probably the only one (besides the maids and staff) to treat her the most
as an individual worth engaging with. And at least never any actual physical abuse, which I honestly would have expected from a brat his age raised to consider someone subhuman. Hell, he even let her indulge in her selfishness at times.