Neoplatonist philosopher Damascius (ca. 480-550) wrote his works a century after the murder of the illustrious Neoplatonist philosopher Hypatia (415). Nevertheless he attempts to pass on without documentation that her death was the result of hidden jealousy on the part of St. Cyril (Suidas Y 166). The subsequent chronicler John Malalas based his information on Damascius.
Cyril could not really have an interest in the murder of Hypatia. She was not a champion of the ancient cults and did not oppose him. Indeed, she had many Christian students, including Synesius the bishop of Cyrene. It is said that she once wrote to him, saying: "I desire to die a Christian" (Fr. G. Metallinos, Pagan Hellenism or Hellenic Orthodoxy?, 2003). It is also said that she was a political adviser to prefect Orestes, which could have lead to hatred on the part of Cyril. But he would not succeed in anything by her death, except only in infuriating Orestes. Though it is true Cyril had some power, nonetheless he was not above the law. Even those who reject the sanctity of Cyril would have to admit that it would have been stupid for him to put himself in danger and in vain to tarnish his reputation or even be punished.
Hypatia was murdered by some fanatical Alexandrians who thought her to be responsible for the rivalry between Cyril and Orestes (Socrates, Ecclesiastical History 7.15 and John of Nikiu, Chronicle 84.87-103). So the perpetrators were NOT the special corps under the command of the Patriarch of Alexandria known as "Parabalani". Moreover, residents of Alexandria were notorious troublemakers (Socrates, Ecclesiastical History 7.7 and Cyril's Paschal Homily, 419). A contemporary source, Socrates Scholasticus (ca. 380-450), says that the murder of Hypatia was initiated by Peter the Reader, not St. Cyril. This is in agreement with the extremely fanatical John of Nikiu (late 7th century). It is worth noting that in the Alexandrian Church, readers were not necessarily priests nor baptized Christians (Socrates, Ecclesiastical History 5.22).
Some people say that Socrates contradicts himself, since he writes that the death of Hypatia "brought not the least disgrace upon Cyril and the Alexandrian church." But the statement does not mean that Cyril was responsible. Rather Cyril was disgraced because of the crime by a part of his flock.
Of course, Socrates is not at all biased in favor of Cyril when he speaks of his innocence, since elsewhere he does not hesitate to point out his errors. Indeed, he had reached the point of blaming Cyril for his folly because he honored as a martyr the fanatical monk Ammonius who was killed after attacking Orestes (Socrates, Ecclesiastical History, 7.14). He felt also that Cyril belonged to the heresy of the Novatians, because he showed compassion to them in his works. However, Cyril considered them as enemies (Socrates, Ecclesiastical History, 7.7).
Furthermore, since everyone knew of the guilt of Peter, maybe we could assume that he did not escape punishment. The murder was a criminal offense under the applicable laws. St. Cyril was not opposed to the punishment of Peter (which could be done, given his rash nature and the arbitration he was used to doing). And it would be foolish to think that Cyril had more power than his "enemy" the prefect Orestes. Let us not forget that Cyril could not save the monk Ammonius from punishment, though he clearly showed that he was opposed to it.
The available data does not support the unfounded assumption that St. Cyril was an instigator of the murder of Hypatia. What is certain however is that the horrible murder of Hypatia is certainly against the spirit of Christianity and is condemned by the Church. We always have in mind that a saint is not born but made. So Cyril, even if he were to have had a share of responsibility for the death of Hypatia, would have became a saint in the later course of his life. Many saints were criminals even before they renounced their sinful life and became fully dedicated to God.
Source: Translated by John Sanidopoulos.