That is why we developed scientific method; it is essentially a means to mitigate against our inbuilt biases. Truth is not something that can be invited in as if it were a next door neighbour. What we can do is make a provisional stab (hypothesis) at what we think might be true, and then test it to death. Your next door neighbour wouldn't like it of course.
But current science tells me that every choice I make is not driven by my real time awareness, but by sub conscious pre determined brain activity. So it would appear that I have to sacrifice my free thought and free will to science and conclude that my perception of reality is all an illusion.
Well, yes, maybe. We don't sacrifice anything to science, of course, but we can try to understand and accept what we have learned from research. Our perception of reality is just that - it is a perception, it is not objective; for each of us our experience is a private fabrication, unique to ourselves only, ultimately unshareable.
I think we must recognise the limitations of science and conclude that there is much more to reality than what has currently been discovered by science. There may well be much more for science to discover in the future, and there may be much that science will never discover. But we should not allow science alone to dictate what is real and what is not.
Science is never a dictator, it advises us. So do we listen to advice or do we ignore it ? We don't have to take prescription medicines, but who is the wiser, the man who takes pharmaceuticals that have been through years of multi level testing, or the man goes to a faith healer ? I see little wisdom in ignoring what we have learned to date, even if that knowledge fails to flatter us or comfort us. Science will never reveal all answers, and in that morsel of humility lies its strength; it is only by accepting that we are mostly wrong, that we can be open to learn. Teachings that claim certainties, on the other hand, are ones that close minds and obstruct real growth and learning.