So after rewatching a decent chunk of the game, I started wondering if 9S hating A2 for killing 2B could have more than one meaning. There's the obvious one of A2 killing the android he loved even though he knew she was about to die from the logic virus anyway, but I did think of another.
Could 9S also hate A2 because she took away his last chance to kill 2B?
I know some supplementary materials talked about how 2B killed 9S countless times without his consent before the start of the game's events, and I also read that 9S trained himself to fight with weapons so he could kill 2B. Since 9S figured out what was going on with 2B at some point despite the mindwipes, he could still hold some resentment towards her. I don't necessarily mean he actively wanted to kill her during the course of the game, but that he might have had a buried subconscious desire for it because of how much she made him suffer.
Adam's line to 9S in Playthrough B could be interpreted as both "You're thinking about how much you want to fuck 2B, aren't you?" and "You're thinking about how much you want to kill 2B, aren't you?"
There are also the lines in Jackass' Research about androids' pleasure centers being tied to combat, with the possibility that their sensations during combat are linked to the feeling of love.
Even though the boss fight in the Soul Box takes place after 9S starts to go off the deep end, it seems to take on another meaning when you know 2B's role in YoRHa:
https://www.youtube.com/watch?v=0cdVnTSdsz0
It shows 2B threatening to erase 9S' memories like she has countless times before, and it ends with him killing her to protect his memories.
There's also 9S' behavior in the Tower when he runs into all the 2B models:
https://www.youtube.com/watch?v=2vatFtgAXK4
He says he's genuinely happy to see them before gleefully shouting he'll kill all of them.
One last reason 9S might have wanted to kill A2 is that she took on 2B's mantle by cutting her hair, accepting her sword, accepting her pod, and absorbing her memories. If 9S couldn't kill the real 2B anymore, killing A2 might have been "the next best option" in his eyes.
None of this is to say that 9S didn't love 2B, but he also might have felt some underlying need to make her feel the same way he felt whenever she killed him.
Considering how many months the game has been out, I'm guessing this idea has been thrown around at some point or another. Then again, I could just be over-analyzing the story and picking on details that aren't actually present.