Yeah, I think all this happens relatively early in the story. I respect the "in depth analysis out of boredom" though.
Kurumi was bedridden twice from the infection in the story; I mixed up the one early in the story with the later one where I thought the plot this "what-if" story was in... The handcuffs should've been a dead giveaway for it to have occured in the first infection attack (atleast that's what I think? I don't remember the handcuffs being there in the later one atleast)
That said, I was solely basing my info on the manga and haven't really watched the anime so my analysis earlier wasn't able to consider the differences of the manga and anime to give a possibility for this situation to occur...
I highly doubt that Miki will do retribution tho since she was also the one to attempt in removing the psychosis in the first place with a clear emphasis on codependency... In the first few chapters..
For the part about the quarantine, maybe in the anime the airborne infection wasn't mentioned? I put that assumption together as I've never seen any clips of the anime showing the college which was the area where the airborne possibility was laid bare, tho the radio site would also be needed to be missing in the anime if that were the case (which luckily, no contradictions yet?)...
Gakkou Gurashi (the manga for what I know atleast) is written in a way where foreshadowing was spread throughout even in the early stages for the buildup of the late part of the story... If anything there was too much detail that just pointed the story's directions to what it is, so it would seem to be quite hard for anyone to just deviate from the original storyline without giving compromise to the original plot...
Since the quick time events were pointed out, I think those would be the best timings to branch off from the original timeline to create a what-if scenario while staying true to the original... I kinda also wanted to see how the girls would tackle that problem but also kinda scared that it would just break my heart... The girls had already went through tragedy and were already developing into greater people... To throw out that progress would probably leave a bad taste... I kinda appreciate the author of the original that they didn't give it such a tragic ending... At the same time, seeing a possibility unfold of how much they could have messed up also just makes me value the story as how it is now.