I think you're misunderstanding how he was torturing her.

Misaki is, or was, a good person (at least Akiho still thinks so). Kimijima was constantly mentally torturing her about being a murderer. He always making her feel guilty about the method used to save them, when there very likely had been a less violent way she could have stopped it. Then, it was when he started manifesting in front of other people and threatening to "haunt" Akiho and Kai while she continued to resist. That last part is what finally broke Misaki and made her submit. Over the next ten years, he continued to harass and torture her mentally. That's a huge amount of time to mentally condition a person. At some point, she basically got brainwashed, and believes in his cause.

This has conditioned Misaki into generally doing what he wants, and over time, allowed him to take her body over (as he did with real-Airi on a more rudimentary level). Kimijima implied that when Misaki mentally withdraws, he has full control over her. But unlike Airi, he currently has a backup with Misaki. The exoskeleton suit she's wearing now (probably one he "encouraged" her to wear during this operation) is something he can control directly through Iru-O, like Mizuka's legs. Now that they are doing things that Misaki might actively want to resist, he can just force her to do them. He also mentioned that the more she resists his control, she might actually damage her mental state, showing how pervasive his control and conditioning over her has become.

You could probably shut off all of Iru-O and reset all the data to a raw state. Or maybe Kona will make a virus that will chase him down and delete his data.