Chances are that in the chaos of the war, the Ushimitsu Institute stole or already had, but they perfected the EC process.
Someone higher up didn't like what Daigiren was planning, so they changed how things were planned to go. Leaving a whole system to take care of the child wasn't the most difficult thing, considering the level of tech they have.
So... fortunately, some people had the moral integrity to not use Saya as a vessel, but they left her as a steward for any possible survivor... or at least for the legacy of humanity.