But given the timing of when all this started, wouldn't her getting rebooted ... not be that bad? I mean it'd still be bad in the sense that the girl we grew to know would have been rewinded, but...
At the start of the game, we wake up with no understanding of where we are, who we are, or who anyone else is.
This is what Maya is afraid of happening to her. It's what the Angels alluded to in the dorm event. Everythiing that made Maya Maya will be gone and replaced with a completely blank slate. And it's possible that this could begin a who-knows-how-long process with Sensei and Maya's roles are reversed, and he's constantly watching Maya get rebooted, each time hoping that THIS time, she'll come back as her old self, and eventually losing all hope that it will ever happen.
While Ayane is often foolish and lives with her heads in the clouds, she has acknowledged more than once that she's not stupid. She knows that getting pregnant is a disaster. If she keeps the baby, Sensei is likely lost to her forever as he gets arrested or conscripted. If she tries to get an abortion, questions get asked, and the one man she's been seen out in public with regularly probably gets arrested or conscripted anyway. There isn't a win scenario if things play out the way they would for normal people.
But Ayane isn't a normal person. She's the daughter of the second wealthiest man in the city, a man who was able to dodge the war by virtue of his wealth, and a man who could, potentially, save Sensei from the same fate. I think Ayane knows this is a long shot. But it's literally the only path forward that allows her to maintain the fantasy of the life she wants to build with Sensei.
But Sensei shot that down before she could even tell him.