free will and agency are two very different terms. Free will is a philosophically charged term that is often incoherent or ill defined, agency is fairly straight forward, it's the capacity of any actor to realize their goals and act autonomously in their own interest. It's the ability to shape your surroundings rather than be shaped by them.

There's plenty of agency in a deterministic universe, a dictator with a nuke has a lot more of it than a slave in a cage. There's no need to be nicer to criminals on grounds that the universe is deterministic, which it is. (both in Newtonian physics and quantum mechanics). The nice guy is as deterministic as the criminal. None of them are "forced to do" anything by their brain state, there is no subject that is puppeteered around by your brain like some reverse dualism, you and I are our brains (and bodies). What matters is if you want criminals to have more agency, and if you don't, you punish them.