Superhappies are dicks, these humans are dicks. We can't impose our morality on the baby-eaters any more than they can on us - they tried to convince us to eat babies because they couldn't force us or wie us out - the implication being that they would have done so if they could. So the babyeaters are dicks too.
I have no problem with the baby-eaters. Battuta's kitten analogy is flawed, because you're talking abour human-on-human interactions. Culture is something we can judge and change, we can, as a species, decide what is right and wrong and impose it on other members of our species. We already do that by preventing murder, rape etc. But we cannot force our morality onto a group that has evolved utterly without it, and outside the bounds of it. Yes, the babyeaters children are suffering, but that's their bad luck for being born into a nasty species. It's neither our right nor our responsibility to change that.
If you acceot that there was no way to both survive personally and save humanity from the superhappies, then the only appropriate course of action would have been to blow the star in the meeting system, especially once the baby-eaters ship was already dead. In fact, the crew of the ship chose possibly the worst option they had available - they killed billions of people, and left the babyeaters open to the kind of species-wide manipulation that they considered to horribly reprehensible for our own species, but somehow it's OK for theirs? Like I said, they're all dicks.