Were the humans "repaired/controlled" actually damaged by the AI?
Max (brainwashed at this point) says the captured contractor was long dead.
However we see him clearly begging them to reconnect him (in his own voice) so the nanobots can regenerate his injuries (which are shown to be fatal). If the AI had taken over his mind and killed him, wouldn't he be dead the second he was disconnected?
And what about the blind dude and everybody else fixed by the AI? Once the AI is infected, they don't just drop dead on the floor, but see to return to their prior unfixed state.
Had they been taken over and killed/assimilated, they would have died, yet they did not.
And it's not like the AI was doing this behind Evelyn's back: it clearly and repeatedly tried to show this to her and explain her all the ramifications of it, but she wouldn't have it.