But how is the mob's Christianity or Hypatia's paganism even relevant, assuming the mob wasn't actually made up of Cyril's bodyguards and acting on his direct orders, and that Hypatia wasn't a Christian convert, and that anyone in Alexandria had any real beef with the pagans - as the conflict was between one group of Christians led by Orestes, another group of Christians led by Cyril, and lots of Jews who were being expelled after their attack on Cyril's group of Christians, which upset Orestes and his group of Christians, along with Jews and pagans.
It was a Christian/Christian power struggle between two very important leaders over Cyril's attempt to encroach on Orestes' power, an early example of the attempt to extend ecclesiastical Christian authority over secular Christian authority (ie., the kings must answer to the Pope). That is purely power politics, and people were being massacred, tortured, and executed on both sides. Hypatia was using her enormous influence to back Orestes Christian authority, so Cyril or his supporters took her out.
As a continuation of the serious conflict, Orestes side of Christianity used Hypatia's murder as a bloody rag, and continued to do so for over a thousand years, getting worse as time went on - with the theme that Catholic authorities are evil, power mad, and murderous. She died because she was an important player in a life-and-death political struggle between very powerful men representing very powerful forces in a very violent city. Cosmos picked a side in the larger dispute, again using Hypatia's murder for political ends.
So, the way Cosmos presented the overall story is that Alexandria was the sole beacon of knowledge and human learning, the only city reaching out to science and understanding, kind of like the city of the Ancients in Star Gate Atlantis. That's ridiculous, because it ignores the earlier existence of all the Greek City States, Persia, the Arabian Peninsula, Judea, Spain, Constantinople, countless other major cities and centers of learning, and the entire rest of the region and world.
And then Cosmos claims a mindless mob burned the Great Library, which is totally false, using the repeated myth to motivate its viewers into readying themselves to form another mindless mob that's ready to act based on stupid myths they learned from watching Cosmos.
And after the mythical burning of the great library, we're drug right back to the murder of Hypatia, this time blamed on anti-science fanatics instead of a particular faction of the Catholic Church.
In the fourth remake of Cosmos we'll undoubtedly be told that John F. Kennedy was assassinated by an anti-science fanatic who was trying to stop mankind's exploration of the moon and beyond.