I was never implying one way would lead to a "game over". That would indeed be poor game design. I was merely saying how events will change, if at all, based on that choice (as far as it looks thus far). You asked, I assume rhetorically, how it could ever be bad to have a herd of zombies you can turn loose on your enemies. Well, you don't control those zombies - The mother does. There are myriad ways that ultimately empowering, if not outright preserving, the Hive could create more problems then it solves. It is much like asking "How could developing nuclear bombs ever be bad for us?". Well, even if you control that weapon today, a time will come, when you don't, or at least others do also. In this case, the MC is not even the one with their finger on the proverbial button, so it seems very prudent to be nervous about the "nuclear option".I don't get the long-term problem part. Yeah, it could go down that way, but does it have to? Wasn't the whole point of at least the second trip (don't remember if it also was the point of the first trip) to try and ally with the hive? Unleashing a zombie apocalypse on your enemies doesn't sound like a bad outcome.
EDIT: While I don't have any idea of *how* it will get resolved further down the road (maybe the way you suggest, maybe some other way), I'm sure that neither choice will lead to any sort of game over, it's just going to affect how the story plays out and who the MC get to fuck and in what way he gets to fuck them. Having an opaque choice lead to an unavoidable game over much further into the game would be extremely bad game design and I've seen no signs of the dev here being that inept (quite the contrary).
In my entirely hypothetical example, I postulated that the daughter might end up as the queen of the hive, in the path where you take her with you in part 1. To follow that hypothetical, I see her being a queen that would be far less of threat to the mutants/MC/life in general, than the mother is, because she has developed an actual relationship with others outside of the hive. Conversely, it is extremely clear, in part 2, that the mother has no connection at all to humanity, beyond being used for breeding and food. Does that seriously not concern you, even a little?