She needs her eyes to be fully complete the battle sequence as she is a battle android re-purposed to be a nurture-droid and raise the remains of humanity on Keplar-22b. We know this as it was shown through flashbacks and story filler between present segments. As she is now the caretaker, Father uses logic to decide his factors as that's his programming but it's clear that Mother has become sentient beyond her programming and taking on the psychological role as a biological mother who will stop at nothing to protect her children. If she followed her programming then the threat (children or otherwise) would have been wiped out a while back to contain the remainder of the flock's good health. In fact at points we are lead to believe maybe Mother even poisoned some of them and killed Father but everything was well calculated for a purpose.
I think there is more at play here, the human race is in turmoil back on earth which is why 2 androids were sent 500+ light years to Keplar-22b (this is an actual planet out there which is thought to be habitable) and as it happens in the late 2100s of Earth time, I imagine they used some kind of wormhole to get there with various fleets (the Arks) following suit to colonise potential planets out there because Earth is no longer suitable as we saw during the flashbacks showing the chosen ones to go onto the Ark.
One faction of humans created battle droids that Mother once was to fight what appeared to be the holy war (religious warriors vs Atheists?) so I imagine it was the Atheists who reprogrammed Mother to become the caretaker of the embryos and raise a pure human race who know no religion so that they grow and continue the race hopefully without the drama Earth's humans created for themselves.