But doesn't freedom of religion have limits when it comes to objective moral good? Say the Aztec religion or the pagan cult of Moloch had survived, would we protect their religious freedom in regards to human sacrifice? Assuming willing victims? 

Why tolerate evil, when it can be stopped through the political system. Slavery was also an evil that for a large part was stopped through the political system, why can't we do the same for abortion which is also an evil?