And yet religious freedom begat liberalism, not the other way around

This doesn't mean religion ought to receive any special treatment going forward. It is a way of looking at the world, but requires belief which is in opposition to other beliefs and they all are in opposition to scientific approach to understanding ourselves and the world we live in. It is also a way of imposing and enforcing morals that cannot be questioned unless one is prepared to face grave consequences. The "priest" of are predominantly men, who are under no obligation to follow the morals they preach and indulge in the "sins" they condemn without fear of prosecution. In the end, when the veil comes off it's about power, money, and sex. So no, no special treatment of religion ought to be allowed in a secular society. And secular societies ought to have laws and mechanisms preventing them from takeover by religious groups.