Earlier quoted context omitted.
Yes, the final chapter. Aside from it being biologically impossible to repopulate from a single couple, it was not really portrayed ambiguously. I don't care to reread it, but from what I remember, the main protagonist was the driving force behind it, grooms her own (single-digit-age?) daughter into the idea, who then sleeps with her own father in graphic detail. He is a little hesitant at first, but relents almost i…
— Spoilers, if you’ve not read this and yet are still reading this comment chain I guess the grooming may start earlier, it’s not really discussed and it’s a bit ambiguous as to when that started > but relents almost immediately, Physically, at the time, though this is something they’ve argued about for 6 years. It’s not a passage I particularly care for, and it could have been less explicit but then I’m mixed on how…
Freezing all alien life is obviously horrifying, and Caroline says as much. It's not as bad as genocide but is treated as nearly as bad.
Flipping the table on Cyberspace is more ambiguous -- it might free those other species on the one hand, but might destroy all life on the other. Lawrence is far more resistant here (though he does eventually relent). But at least in this case the dilemma serves to hammer home the central point of the story: that life is given meaning by challenge and striving and that removing all limits is the existential equivalent of mainlining heroin. It's a provocative idea, but there's at least a point to it.
The incest stuff, though, is completely unnecessary. There's no reason why breaking Prime Intellect would result in the two of them (and only the two of them) existing in an empty world. It's a totally artificial scenario, seemingly contrived to set up an excuse for endless incest, even though that wouldn't work biologically. It might make sense if there were some sort purpose for it, or if it were treated as a horrifying dilemma. But he portrays it as this sweetly innocent thing that is primal and right, and it's shown to work flawlessly to set up a harmonious and healthy society superior to both the old world and what Prime Intellect built.
Again, I love most of the story and revisit it every few years, but this ending is thinly-veiled fetish gratification with no redeeming value.