There is an infinite qualitative difference between physical processes that are subject to physical laws and hence cannot transcend those laws and a conscious being who can be self-aware and act with intention.
The project of a rationally derived ethical system has been shown to be a fantasy. Not only does it presume that such a universal system could be formulated, it also presumes that people could act according to such formulations.
It is true that Muslim thinkers are tilting in the direction of increased integration and participation in civic life, and this has implications for their willingness to question traditional attitudes.
While it may be hoped that an equitable balance between personal freedom and public duty will produce a civil society, the tenets of liberalism turned libertarianism will always tend to undermine such a balance.
So the state would get to decide if a Jewish school can refuse to hire a Muslim maths teacher (and vice versa) and whether a Christina church can refuse to hire a Buddhist as a youth leader or pastoral care worker.