I believe Harris's view is that we are still justified in imprisoning people for consequentialist reasons, just not based on a "moral desert" theory.
I'm not sure I follow. But in any event, I was thinking of "free will" and "moral responsibility" as definitionally connected (following a convention I picked up reading about the topic). That is, I'm morally responsible for my actions if I undertook them because of my free will. And my will is "free" in the relevant sense if I can be held morally responsible for my actions. But I'm not attached to the "responsibility" talk; everything in the above can just be reframed in "free will" terms.