1) People act according to past experience, environment and internal biology. 2) People environment also consist of the knowledge that "For any given situation there are many options and if one looks hard and tries one may choose an appropiate response". If the society emphasize on this aspect a person might be more willing to make a "choice". Of course not everyone will respond the same way to this knowledge.
1) doesn't imply that there is no "choice" and 2) doesn't imply that we are not "programmed" to behave in certain ways. Actually it might be that 2) is helping us to "program" people in certain way.
In the context of "crime and punishment", as we get better at 2) or someother scientific development we can reduce the need for "punishment".
The best analogy I could think of explaining the above language play on mind is following. Say you are training a new chess player to improve the game. You can say one of the two things: 1) For a given board position there are limited options. 2) For a given board position there are many options.
While both being true on thinking deeply they can have different effect on the person. It also matters what we emphasize. For a person thinking less 2) may be better thing to emphasize. For a person thinking lot 1) may be better to emphasize.