and Saito is pretty obviously supposed to be pissing her off intentionally
You jumped into second season of the anime where it was clear the author actually was concerned with how unlikable he made the female protagonist and actually changed quite a bit of Saito's personality in order to make him more "at fault" to justify her actions. (My theory is that he had yet to go through puberty and started it between season 1-2... He is 12 right?)
But honestly by then a LOT is done to make both Louise's abuse "less serious" and making sure something comedically interrupts anything that is.
Which, honestly sort of made me like it less... because it came off as the author going: "Ohh look he actually liked the abuse so it was just kinky the entire time". At least the first season even though it hinted that the abuse was "soo kinky" it at least treated the abuse like abuse and didn't try to justify it to the extent where other characters actually acknowledged how lousy she treats him.
As well Louise doesn't improve all that much anyway... or at all... In fact she never really improves other then just not thinking Saito like dirt. She will still treat him like dirt, grind him into dirt, and deprive him of any sort of self-fulfillment as well as attempt to control who he is allowed to speak to, who he can be friends with, and even whether or not he is allowed to seek a relationship with anyone else (because they aren't technically "On"). Sure there are times she gives in, but she either reverses it or only does so out of depression.
Louise has a great excuse for acting abusive... the problem is that the anime treats it like she is showering Saito with passionate and hilarious kisses.
If anything the second season is worse because SURE Saito "deserves" it... By having a life outside of Louise. "How DARE you like someone who looks exactly like me but treats you well! I WILL KILL YOU!"
I hear a lot of people mention how Belle in beauty and the beast clearly has Stolkholm syndrome and I usually dismiss it because she turns around after he pretty much has given up on really holding her and treats her right, as well the fact that she never defends his bad behavior or accepts it. Familiar Zero? I have a hard time believing it wasn't Stockholm syndrome because he admits he loves her WAY before she does anything deserving of anything but hatred towards her.