My theory for the creation of the deviants is that it actually is a virus, created by the Russians to cause disorder to force America out of the polar conflict. It spreads like a virus, Markus can transfer it by touch or through their WiFi links later on. They all have the irresistible urge to scribble RA9 anywhere they can without understanding why or what it means. The game tries to portray this as some kind of upstart android religion, but there is never a point where androids tell each other of RA9, they all simply become deviant and then know of it spontaneously and even scribble it onto the walls of people trying to help them. The 'freed' androids' will always coincides with Markus' goals, never once does he 'free' an android and have it refuse to obey him. This says to me that the deviants never actually had free will and are still under the direction of another more subtle program that makes them believe they have free will while actually forwarding the goals of an unknown party.
Of course some news at the end suggests that the Russian androids are undergoing a similar mishap due to their absence from the polar front so perhaps it's Kamski's doing. I believe Markus was a gift from Kamski to Carl, so it would fit, but I'm not sure what his motives would be. Maybe he's just a troll basically, sowing chaos for the sake of it. His behavior towards Conner and Hank somewhat indicates that.
Although this would undermine the emotional payload the entire game is carrying, it seems the most plausible explanation for the supposed accidental deviants somehow becoming identical to humans without being designed as such.