This was terribly interesting, I'll be re-reading it in a few days to see what I can pick up that I missed the first time through.
I'm not so sure we can so easily label these two endings the good and bad endings. In one, humanity (or at least what humanity evolved into) goes along with the superhappies, and in the other, they do not. Certainly, going along with the superhappies is not a good solution. We give up much of what we consider to be vital to our identity, and in return, the superhappies make their spaceships look nice. Now, the superhappies are also modifying themselves, arguably just as much as humanity is, but even if they lose (their perspective) as much as we lose (out perspective), we don't gain (our perspective) as much as we lose.
The true ending is about resisting the transformation. But they seem to accept an... unintuitive tradeoff while doing so. They trade the lives of a few billion humans for the ability to allow the superhappies to do to the babyeaters exactly what they intended to do to the humans. In fact, unless I missed something, I don't think taking this trade was ever even questioned, it just seemed that taking the trade and sacrificing the people to so that the babyeaters would be transformed exactly like humanity would have been was just common sense to them. Now, I can see how the characters in the story could perceive this choice as righteous and moral, but it seems to me to just be a another tragic ending, just in a different flavor. A tragedy due to a massive failure of humanity's morals, rather than a tragedy due to the loss of pain & suffering for humanity.
As an aside, the construction of the two (three?) alien species, with their traits, culture, and thought processes was superb.
Well, I re-read it, and now neither ending seems so tragic anymore. I now think that there is utility in transforming the babyeaters that I didn't see before.
That said, the way they went about their supernova operation seems illogical, particularly the part about giving them 3 hours and 41 minutes. I would imagine they decided on that amount of time by estimating the chance of the superhappies showing up as more time passes times the disutility of them stopping the operation, vs the number of humans that will be killed by the supernova as more time passes, and choosing optimal time.
It seems like relatively few humans are able to escape prior to around the 8 hour mark, and, given that the superhappies gave no indications of when, if ever, they would follow (before their operation with the babyeaters was finished), the best times to blow up the star would be either immediately, if the chance of the superhappies showing up is judged to be high, or the disutility of transforming all the humans is high (relatively speaking), or they would wait 8 hours and save most of the people on the planet. Waiting about half that time seems to be accepting a significant risk that the superhappies would show up, for not much gain, while waiting about another 4 hours seems to be about the same risk again, for a much larger gain.
Still though, a very good story. I expect I'll continue to stretch my mind now and then contemplating it.