Many people in this forum clearly doesn't understand Koto's suffering from that PTSD and we will see them come at her soon after reading the last chapter.
It's like this every time a character is clearly mentally ill, sadly. They seem to expect rationality all the time, even if the story depends on the character's current lack of awareness or control over their behaviour.
Koto is clearly not doing this out of malice, she's probably not even aware that the way she is acting about it is toxic and will impact both of them negatively later on. She can't help but worry that Aya will disappear again, so this is her attempt at keeping the girl safe and close to her.
Koto's entire problem is that she is deeply scared of being abandoned and can't move on, and really, who would be well if their girlfriend suddenly disappears and then comes back a few years later the same way they were before? It's a very... unusual situation that can't be treated as if it had only 2 right answers.
No, it's not that the way she is acting is good and correct, but it's to be expected when she is mentally ill, never got over her love and never learnt how to deal with her feelings. You don't become an adult and wake up knowing everything about life ever the next day. She's not evil or manipulative for that, neither are the other characters for wanting to move forward.
As the other poster said, those events are most likely going to culminate into her exploding and I'm very excited for it. She'll have to learn the hard way that she can't keep Aya caged, and that the best thing to do is allow her to recover from the 7 years she wasn't there, meet others her age and in a similar situation, just like the boy.
I don't think that this will have a fully happy ending anyway. Koto's fears aren't completely baseless when Aya could very well disappear again, if it happened once, it could happen again. We don't know the cause, how it happened... So it makes sense why she thinks keeping her in a safe, closed space under her watch would be the best option. They love each other and are forced to be in an abnormal and unhealthy situation, a lost child living with someone seeping poison, unaware that she's bringing harm and possibly ruining their relationship.
The characters are human and expecting them to be perfect and act 'in the proper way' all the time is boring.
It sucks that every time a new chapter comes out it's always the same "this character BAD and is doing that because BAD!" and I won't deny that I'm contributing to that by engaging, too.
Let them get into trouble, pay for it and learn from their mistakes or maybe even become more messed up!
I think all of them have good reasons for being the way they are.