The criminal justice system can still function without the false premise of free will and agency, and without the false premise that someone with a brain tumor magically has less agency than someone without a brain tumor but who has some more complicated and less understood problem with their brain.

It can be premised on concepts such as rehabilitation (which I believe mostly can't happen with murderers), deterrence, creating a sense of fairness in society (which builds trust), protecting people from the murderer, and so on.