To me it seemed kinda obvious that Hive girl was set up to be the new queen, because the hive queen called her daughter, if I remember correctly, and she seemed to be the only other hive mutant beside the queen with a personality or will of her own. So I took her back to the vault, because she didn't seem to like the way things currently are with the hive, which is probably why she ran away from there in the first place.
I expect Hive Girl to gain control as the new overmind somehow, if the old queen is dead, which would be a very powerful ally for the mutants.
It's going to be interesting how this branching in the story will be handled. As it stands now the mutants are too weak for open conflict with Zeta, but being in control of the hive could change that. If this depends on the choice of taking Hive Girl back to the vault or leaving her, then I wonder how the mutants would move forward without the help of the hive.