There is a perfectly valid and functional world model that incorporates both the science and it's atoms and spirituality. Functional in a sense that people having this view can both apply their knowledge to the scientific domain (building new mechanical machines) and also to the spiritual domain, that is be truly happy and enlightened in the way the experience their own life. (Seeing yourself (factually incorrectly) as ONLY a chemical machine does not produce happiness, mission, love, etc. (nor good health for that matter, because health is affected by psychological wellbeing a lot) without a solid spiritual foundation.) Jordan Peterson has a very good video about this, something about reconciling science and religion.
The point is, "Free Will" is not a scientific concept, it's a concept from spirituality. And can very well fit with all of the science that is known to humanity today. Free will comes not from the randomness of quantum mechanics, but from implications of the chaos theory (which has basically killed determinism as a means of understanding the human life experience).