They have managed to restore about 10'000 in 3 years. Out of 5 billions, and even those needed to be placed in therapy. That's not counting that weaker individuals were melted completely without preserving their psyche.
In 50 years, the ones who knew those people and/or cared about their restoration would be gone. And those recovered would still be missing their family members and loved ones that were not.
Yeah, no, it would be faster and more humane to repopulate the world via an old and tried method than to mend the cup that was so irreversibly broken. For all intents and purposes, the humanity of Earth-2 was nearly wiped out.
Well, considering the high level of tech allowed mind-uploads, clonation and cybernetics, the average lifespan should be way longer than what we have now, if not effective "quasi-immortality". For the therapy thing, being able to edit/modify their memories would also speed greatly the process. Lastly, to fill the gaps Earth-2 could adopt people from the original Earth or the other space civilizations. Failing that, a careful eugenic program with mass-cloning, genetic manipulation and artificial wombs would help to solve this problem as well, for not to mention at the same time the average genetic quality of mankind's DNA would receive a much necessary improvement. And that's not taking into account Senya, who assuming he did return at the end, possesses his "anime genius" to solve any problem given enough time.
In any case, all of this is beyond the purposes of the original story.
As for who is responsible for that mess, that's really hard to quantify. Obviously, it was evil!Senya, but that's not saying much. It was Senya's fault for getting stuck in VR, it was Shulgi's fault for coming up with an experiment with such a huge failure state and missing vital clues before committing to one of his plots, it was the cultist faults for creating evil!Senya to begin with, and the finger-pointing can go forever. But ultimately the Masters were the ones who engineered the situation, and evil!Senya was acting out of fear for the inevitable exterminatus of 'data' that would follow the current iteration.
Well, it is true that everyone is guilty of something, but the cultists are the most guilty ones, if only because they were directly responsible for the creation of Id-Senya, thanks to their absolutely evil nature with no redeeming qualities which ensured the boy was subjected to constant trauma and abuse. Should he have been raised in a more humane environment, most likely he wouldn't have had such extreme reactions and deranged mindset.
Also, I thought he wanted to destroy the reality he was inhabiting because he believed it was a false one. He was correct with that, but he admitted he wasn't sure if his plan would really work or that what he would accomplish was a spectacular, disastrous backfire.
Either way, what's done is done. Good CYOA overall. I would have preferred that the "perfect world" ending won, but it would have been a bit OOC for the main character.