Re: This is all very fine, except for one thing.
Same AC as before.
Did you read anything about the entire issue, or did you just skip it to jump into proudly proclaiming your disdain of "archaic superstition"?
Monica Cellio is/was one of the most prominent long-time moderators on SE. One of the three major site that Cellio used to be a mod at was Mi Yodeya. Three guesses at to what that Q&A is about?
Everyone who is involved had to know that Cellio is observant of both Sabbath and the subsequent holidays. This means they knew when she was going to be offline, just as you would know that your Jewish/Muslim/Hindu/Catholic/Orthodox etc. etc. coworker is unavailable on some days.
To spell it out for you even more bluntly - SE went with an unprecedented action, while giving an unpaid, multi-year contributor exactly zero possibility to defend themselves from both the fallout of the decision and the associated all-but-slander.
Surely even you, with your apparently Hot-Topic brand of atheism (and I say this as a vocally anticlerical atheist myself) would see the assholery inherent in this context?
Finally, note that I did not say that the first incident was outright bigotry. In the OP, I described how the subsequent actions by SE caused a reevaluation of my opinion in that direction. It's hard to give someone a constant benefit of doubt when they repeatedly use up their credit.