This may be just trivial nonsense, but wasn't it explained in S1 that Allelujah was put on that transport ship with the other kids because they were failed experiments (or whatever) and thus would be disposed of? While in S2 Allelujah says that the kids stole themselves the vessel in order to escape. They probably knew that they were going to be disposed of though.

It would seem like a waste of a ship, unless the HRL Super Soldier facility wanted to enjoy some survival games.