I had the sneaking suspicion, back in "The Hive Part 1", that leaving her would yield short-term benefits and long-term problems. After doing both routes of "The Hive Part 2", I feel that suspicion is all but obvious now. I noticed that the mod has removed any suggestion as to which path to take at that juncture, which I think is the only viable thing currently, but I also think that anyone who decides to leave her will eventually be restarting from that point once they find themselves in a post-apocalypse zombie apocalypse.
Of course, the other possibility is that, after taking the girl with you, and leaving "The Mother" in part 2, you eventually end up striking the same deal with her, or "The Daughter" becomes queen and you breed her instead, and the ultimate outcome to that situation is basically the same either way. I suspect that is probably what will occur, as otherwise every event of the upcoming war will all be radically different based on that one choice, which would make far more work for the dev. This game is already ambitious enough without the prospect of adding in two completely divergent paths for everything that follows, so it seems most likely that the Hive ends up your allies either way. The only real choice seems, to me, to be if you feel forcing "the daughter" to be enslaved by the hive, is worth saving Keen's life. It also seems likely to me that Keen will never recover, mentally, and may actually pose a danger to the mutants going forward.
Any certainty that leaving the daughter at the hive is "the best option", seems silly, for now. Choose what "feels" right to you, and live with the results (which, frankly, is stellar writing by the dev).