Many years ago, a freak was someone who was deformed, had an unusual physical abnormality, etc. A women with a beard was a freak, a boy with a tail was a freak, a man with two heads was a freak, and so on. In time, a freak became a person with an obsession or overwhelming interest in something. Maybe you know a neatness freak (everything must be very clean and in its exact place), a Beatles freak (someone who reads everything possible about the Beatles, has a collection of CDs and records, etc.), and so forth. The word is used humorously.
Control freak is a little different. It began as a slang expression but is now accepted in formal English.