yet being able to...still acquiesce to religion when its followers demanded that they alone were the guardians of morality.

It wasn't true--the religious (and religions) don't have any more insight into where moral intuitions come from than does anyone else, and we've known it's logically bankrupt at least since Socrates (not that many haven't tried to rescue it!).

But in this, religion has played the role of the fallen villain who, though defeated, gets the protagonist to lower their guard out of empathy for long enough to deal one last vicious blow in revenge.

I hope we can recover from the wound. But it's a bad one, because in ceding morality to religion we are decades, perhaps centuries behind where we should be in understanding what morality is and what makes a good society for humans (by some marginally justifiable definition of good, not sky-father-wills-it).