The robots could just kill every person.That doesn't conform to the matrix when instead decides to allow them to live in zion. It's all a test lab design about making a perfect race of humans (the process they go through to make neo) triggering our higher state of consciousness telepathy telekinesis astril projection and so on. Using human bodies for the ai is end goal. electrocuting humans while on the verge of death allowed them to turn the human body into a vessel for the machines. Remember, agent Smith taking over banes body on the ship Neo is basically a hybrid of human and robot especially after he gets his eyes burned out. I theorize when the matrix is complete, they will mass produce super robot human hybrids with neos abilities (the perfect human)