My problem is, its easy to tell a drone to attack a ship. Each vessel, I imagine, carries unique signatures; heat, weapon and engine trails, comm systems, etc. Telling a drone to attack a person, well, they'd need the ability to differentiate between humans.
That being said... if AIMEDs can tell the difference between humans and diagnose their illnesses, perhaps there's a system by which organic bodies can be told apart. Again, heat signatures, facial and retinal scans, that sort of thing. However, in combat, these would be incredibly difficult to implement. Soldiers wearing any kind of combat equipment would probably lose their defining features. Friendlies could be given strobes to keep them out of harms way, but, if that were the case, I imagine combat drones would be something like shock troopers; turn on your strobe while the thing starts turning on the heat signatures that don't have one.
Still, it's EVE, so its not as if you don't have room to say the system works via technology we don't understand in the modern age. That ocular implants can process images as quickly as a human eye says something for the analytic systems in existence in the cluster.