By “Free” Root means autonomy. She wants The Machine to have control of itself, and not be under Harold or the governments control. Harold has taught The Machine the value of life and to have a strict moral code, so there’s no big fear of a Skynet situation from Her. What we don’t know at this point is what Samaritans been taught, if anything, other than how to gather information to predict behaviour. Plus the fact that it’s an open system. Ask any question, get any answer. At least The Machine has safe guards against the government being able to do that.