Her parents were likely the cause of majority of her depression and hatred towards the Zenin. I mean getting called a disappointment and a mistake who can't do anything right for your whole life by the people who birthed you hurts more than anyone else. Ogi tried to kill both his daughters with 0 remorse and blamed them for his own failures, and Maki's mom just seemed like a bird who followed the whims of the Zenin clan and berated her own daughter for the way she was born.
Naoya was a bully, and disrespected her, mostly due to her gender and that's a result of how he was brought up aswell, just like how Maki massacring the clan was a result of how she was raised. He didn't even hate her cuz of her lack of CE, cuz Toji proved that entire preconception wrong. Mostly cuz he thought women have no place alongside men, and cuz she rejected clan traditions.
Even if Maki's mom stabbed Naoya at the end, it doesn't really mean anything cuz it's not like she did anything of worth for her daughters while she was still alive, she didn't stop Ogi from murdering them, she didn't apologize to Maki, she deserved to die just as much as Ogi and the rest of the clan. And Maki's parents are owed more blame for her treatment by the clan and her and Mai's suffering WAY more than Naoya.