The scientific method is just a way of acquiring new knowledge, not a way of organizing society or deciding economy/policy/laws.
That's where you are dead wrong.
You can't use the scientific method to decide if a man has to go to prison or not.
As I already stated, the matter of ethics is for another discussion. But yes, you can, and, in fact, if you study the science of human behaviour you see that prisons are highly detrimental for societies.
If you want to deal with criminality and prevent it, I suggest you study the scientific literature in that reagard. A few names.
Gabor Maté is a Hungarian-born Canadian physician who specializes in the study and treatment of addiction and is also widely recognized for his unique perspective on Attention Deficit Disorder and his firmly held belief in the connection between mind and body health.
James Gilligan is an American psychiatrist and author, husband of Carol Gilligan and best known for his series of books entitled Violence, where he draws on 25 years of work in the American prison system to describe the motivation and causes behind violent behaviour. During his career, Gilligan has served as director for the Bridgewater State Hospital for the criminally insane, director of mental health for the Massachusetts prison system and President of the International Association for Forensic Psychotherapy. He now lectures at the Department of Psychiatry, New York University.
You can't use the scientific method to decide if we ought to build nuclear power plants or solar cells...
If you don't understand how wrong this sentence is, then there is nothing to talk about. You simply have no idea how the scientific method works.