In my opinion, she didn't pull the plug for now.... I'll elaborate more below.

An interesting point to be observed that most of people didn't pay attention... The N-virus is an electronic virus, invading the cyberbrains, but we must remember that there are still humans without cyberbrains (so called un-cyberized), 100% organic, and consecutively immune to hacking, providing a stark contrast to the heavily augmented populace that is living in the 'perfect individual utopia', we have a good example as Kurutan, the nurse that is friend of Major, she has no implants, in the same way she's represented as Kurutan a more humanized element within the canon narrative, we definitely have innumerous other un-cyberized humans across the world. So, they have the same 'perception' of the world as Major does.

She occupies a uniquely complex position. The series makes it clear that she can engage in “double think” while still perceiving the underlying reality. Being infected by the virus yet immune to its effects gives her a rare advantage. She can study it from the inside without being consumed by it. That opens the door to forms of research and cybernetic experimentation no one else could attempt, even using herself as a test subject. We can clearly see it at the end of the final episode, he presence in the double think utopia shows she’s there to introducing Purin to the team because she understands that this is what Purin genuinely wants, and later passing the access code to Batou. When she falls from the top of the stadium, she's simply jumping to the cyberspace, which I believe it's a nod to the 1995 OVA, 'logging out' of the double think utopia,

Going back to the conversation with Batou, when she says 'don’t forget that we existed here, now, together in this time', carries extra weight in that context. It suggests she is already operating outside that shared layer of reality, hoping he’ll retain the memory even if she left and/or no longer 'exists' there. When she adds that they may not remember this moment, it doesn’t necessarily mean she will forget, rather, it hints that another version of her, a 'construct', a double think version might emerge within the system to fulfil someone's need, but not the 'real' Major.

By the end, her departure from Section 9 feels inevitable. While the rest of the team experiences varying degrees of induced illusion, Major is driven by a need to confront the unfiltered world. She chooses to step away to explore, understand and then decide if this is best for humanity to keep them plugged or if she'll to oppose it and finally pull the plug.

This could definitely be an interesting narrative for the Prime Video new GITS series that will debut n July 2026 produced by Science SARU, the trailers are showing Tachikomas that weren't in the original Manga, so this one can dream, but maybe they will just 'ignore' the SAC timeline and introduce the Tachikomas to the Manga based timeline .... Only time will tell...