I watched this movie many times. I replied in detail some of perhaps the biggest questions people face regarding the question of Hypatia and her murder:
Is this the true account? The Life of Hypatia
By Socrates Scholasticus, from his Ecclesiastical History
Reprinted with permission from Alexandria 2
THERE WAS a woman at Alexandria named Hypatia, daughter of the philosopher Theon, who made such attainments in literature and science, as to far surpass all the philosophers of her own time. Having succeeded to the school of Plato and Plotinus, she explained the principles of philosophy to her auditors, many of whom came from a distance to receive her instructions. On account of the self-possession and ease of manner, which she had acquired in consequence of the cultivation of her mind, she not unfrequently appeared in public in presence of the magistrates. Neither did she feel abashed in going to an assembly of men. For all men on account of her extraordinary dignity and virtue admired her the more. Yet even she fell victim to the political jealousy which at that time prevailed. For as she had frequent interviews with Orestes, it was calumniously reported among the Christian populace, that it was she who prevented Orestes from being reconciled to the bishop. Some of them, therefore, hurried away by a fierce and bigoted zeal, whose ringleader was a reader named Peter, waylaid her returning home, and dragging her from her carriage, they took her to the church called Caesareum, where they completely stripped her, and then murdered her with tiles.* After tearing her body in pieces, they took her mangled limbs to a place called Cinaron, and there burnt them. This affair brought not the least opprobrium, not only upon Cyril, but also upon the whole Alexandrian church. And surely nothing can be farther from the spirit of Christianity than the allowance of massacres, fights, and transactions of that sort. This happened in the month of March during Lent, in the fourth year of Cyril's episcopate, under the tenth consulate of Honorius, and the sixth of Theodosius.
* The Greek word is ostrakois, literally "oystershells," but the word was also applied to brick tiles used on the roofs of houses.
Whether you're pagan, Jew, or Christian, in Alexandria, there was at that time for whatever may be the reason a highly volatile situation, where three groups seemed to mutually hate each other. Particularly, pagans have for a long time before been quite violent and deadly against many Christians. As Christianity became stronger, and politically having the upper hand, it seemed that some Christians decided to believe in a vengeful understanding of their suffering in the hands of pagan terrorists by terrorizing their descendants. St. Cyril's writings were never for that, and in fact, even when people complained that they didn't have the clemency to love their neighbor, he said that is why it is necessary that you should pray and have the Holy Spirit enlighten you to forgive and to love your enemy:
The blessed Paul speaks the truth where he says, that "if any one be in Christ, he is a new creation:" for all things have become new, both in Him and by Him, both covenant, and law, and mode of life. But look closely and see how thoroughly the mode of life here described becomes those holy teachers, who were about to proclaim the message of salvation to every quarter of the world: and yet from this very fact they must expect that their persecutors would be beyond numbering, and that they would plot against them in many different ways, if then the result had been that the disciples had become indignant at these vexations, and wished for vengeance on those that annoyed them, they would have kept silence and passed them by, no longer offering them the divine message, nor calling them to the knowledge of the truth. It was necessary therefore to restrain the mind of the holy teachers by so solemn a sense of the duty of patience, as to make them bear with fortitude whatever might befal, oven though men insulted them, yea and plotted against them impiously. And such was the conduct of Christ Himself above all others for our example: for while still hanging upon the precious cross, with the Jewish populace making Him their sport, He put up unto God the Father prayers in their behalf, saying, "Forgive them, for they know not what they do." Yea, and the blessed Stephen too, while the stones wore smiting him, knelt down, and prayed, saying, "Lord, lay not this sin upon them." And the blessed Paul also says, "being reproached we bless, being reviled we entreat."
The exhortation of our Lord therefore was necessary for the holy apostles, and most useful for us also, to oblige us to live rightly and admirably: for it is full of all philosophy. But our mistaken preconceived ideas, and the fierce tyranny of our passions, render it a thing difficult for our minds to accomplish: and therefore knowing that the natural man does not admit of these things, regarding as folly and mere impossibilities the oracles of the Spirit, He separates such from those able to hear, and says, "I speak unto you that hear and are prepared readily to perform My words." For the gloriousness of spiritual fortitude is displayed in temptations and labours. Imitate therefore in these things Christ, "Who when He was reviled, reviled not again, suffering He threatened not, but committed Himself to Him that judgeth righteously." But perhaps thou wilt object, saying within thyself, 'Christ was God, but I a frail man, having but a feeble mind, and one unable to resist the attack of covetousness and pain.' Thou speakest rightly: for the mind of man easily slides into wrong doing. Nevertheless, I say, The Lord has not left thee destitute of His compassion and love: thou hast Him by thee, yea within thee, by the Holy Ghost: for we are His abode, and He lodgeth in the souls of them that love Him. He gives thee strength to bear nobly whatever befals, and to resist manfully the attacks of temptations. "Be not overcome therefore by the evil, but overcome the evil in the good."
When I read this sermon, it seems to rebuke exactly what the characters in the movie claim to be complaining about, "Christ was God; we can't forgive the way He did." St. Cyril speaks directly to them, "The fierce tyranny of our passions." He doesn't sound like someone who's talking to peaceful Christians. If it was the second or third century, someone would talk about patience and persistence and the rewards of eternal life for enduring persecutions. But in the fifth century, St. Cyril seems to be talking to those ignorant monks who did indeed kill Hypatia, and because of the chaos of the time, sadly, St. Cyril just couldn't control them enough. There is no evidence at all that St. Cyril would order or support such violence. He spoke of forgiveness for the Jews, as well as for the Gentiles. How else, he implied, can we spread the love of the gospel if our terrorizing passions get the best of us?
There is truth to the story of Hypatia, and it rightfully did bring shame to the Church of Alexandria. But this doesn't mean the Church endorsed such thuggery. Alexandrian bishops were the top educated and most open-minded, and knew of the several sciences and philosophies. But there are times when things get out of hand, and these were one of them. Unfortunately, many people, whether it be atheists in the West or Muslims in the East, like to capitalize on this, the former using the story as a thorn in Christianity, and the latter using the story as a justification to Islamic Sharia, and both simply love to use fictionalized rewording of the story a century after the incident (written by an apostate from Christianity) to try to support their agendas, when in fact, even the Church herself condemned these actions always, even St. Cyril condemned these actions.
Finally, if ST. Cyril was really responsible, do you think Nestorians would let it go? They would have used this as a stabbing point to destroy St. Cyril's reputation. But neither the Nestorians, nor Orestes the governor (who didn't like St. Cyril) pressed the case any further with him. If the case was to be pressed further, the emperor wouldn't hesitate to put St. Cyril to prison, as he did after the council of Ephesus. These monks were probably duly punished for their actions, and life moved on (and then Nestorius shows up).
It is not fitting for us, who are inclined toward piety in God, to be armed with swords but rather to be patient. Even though some people want to persecute us, we must reproach them to be good. We must be patient but never silent, as we must refer to Him who judges rightly. — St. Cyril of Alexandria, Glaphyra on Genesis 5.4, 5.
I think his sermons and writings here speak for themselves.