Locking people up is something we've known how to do for millennia; we're not quite as practiced at understanding human psychology and neurology.

Minor quibble: my understanding is that, in European-derived cultures at least, prison time as a punishment for crime in its own right is actually a relatively recent (i.e. post-Enlightenment) development. We've locked people up for millennia, but the victims have usually been political prisoners, prisoners of war, or people awaiting other forms of punishment.

Not that this really degrades your point about deterrence and incapacitation being easier to implement than rehabilitation.