The question has to be more sharply defined than this. Is it just the human brain that has to have free choice, or is it being alleged that freewill is a psychic property that rides above the physical workings of the brain?
So if the brain is, for argument's sake, some kind of determistic machine, does that matter if it is also isolated enough from the world so as to be free to entertain local choices?
Being a complex machine, it could make complex choices. These choices would be determined largely by the machine's own internal states - its memories, habits, expectations, needs, goals.
So what exactly do you want to claim freedom from? Freedom in the sense of local autonomy in the face of global constraints? Or freedom of the mental from the physical? Or I guess there is the third thing of freedom from physical simplicity.
On 1), we clearly enjoy a measure of practical personal autonomy. We may be constrained by our social and material contexts - the world is what it is - but there is little reason to believe we are acting like programmed robots.
On 2), unless you want to argue for immaterial souls and other unscientific notions, this part of the argument probably usually boils down a concern over attention vs habits. Our own body seems to act on reflex and automaticism a lot of the time - if "we" let it.
But neuroscience tells us this is really just degrees of freedom and willing. When we act out of habit, we are both more constrained and more free. A habit is a routine learnt over time and so strongly constrained by prior experience. Yet habits are also very freely emitted. The brain just let's a stored action pattern go on the basis of triggering input.
Attention on the other hand is reserved for handling the novel or difficult. There is less experience to constrain our response, and so more time is taken to develop a plan.
But is there any real difference in terms of autonomous choice whether a brain is acting on the basis "this is what I usually do in these circumstances having thought about it many times before" and "this is a bit new and I have to spend time thinking it through now"?
On 3), this is where perhaps the most angst about microphysical determinism (or indeterminism, or randomness) arises. We don't want to be thinking of ourselves as being as physically simple as the world around us. We want our brains to be independent of this kind of causal simplicity.
And given that the brain, even if we view it as a machine, is a really, really complex machine - the most negentropic concentration of matter in the known universe - then where is the heat in the argument? Our own neural complexity makes us hugely isolated from the simplicities of the physical world, especially from the highly generalised view we take of the microscale in our material theories.
So how much freedom is enough freedom? Do we need absolute freedom from external constraints? Do we need absolute freedom from our own developmental past (in the shape of accumulated habits and expectations)? Do we need absolute freedom from physical simplicity?
I'm not saying determinism or computation are actually the right models to apply here. But even if they were, they don't seem to create ontological paradoxes unless you are demanding some kind of absolute isolation of mental self from material self.
If all that actually worries you is the relative isolation of the material self from material world - the freedom to entertain and make choices - then we clearly have that both by evolutionary design and differences in physical scale.