Hypatia clearly lived during a power struggle between pagans and tolerant Christians on the one side, and dogmatic Christians who demanded the final destruction of paganism on the other. Hypatia herself was a pagan, but was respected by many Christians, and exalted by some (though by no means all) later Christian authors as a symbol of virtue, often portrayed as a life-long virgin. These later accounts should not be seen as strict historical records, though, as they often contradict each other.
Her contemporary Socrates Scholasticus in his Ecclesiastical History portrays her as a follows:
Some insights into the power struggle of the time are granted by the letters written by Synesius of Cyrene, Bishop of Ptolomais, to Hypatia, whom he loved and respected as a teacher. In one of them, he complains about dogmatic thinkers: "Their philosophy consists in a very simple formula, that of calling God to witness, as Plato did, whenever they deny anything or whenever they assert anything. A shadow would surpass these men in uttering anything to the point; but their pretensions are extraordinary." In this letter, he also tells Hypatia that "the same men" had accused him for storing copies of "unrevised copies" of books in his library. This indicates that books were rewritten to suit the prevailing Christian dogma. 
The possibility of forged documents is important, as it makes it hard to get accurate information about Hypatia's later murder. Theories range from a local, spontaneous Christian uprising tolerated by the Christian patriarch Cyril over a conflict between Cyril and the more tolerant prefect Orestes to a conspiracy supported by the Emperor himself. Another point of view holds that Hypatia was part of a "rebellion" and her murder unfortunate, but inevitable. John, Bishop of Nikiu, a 7th century author, described her death as follows :
Socrates Scholasticus complements this account by stating that, while she was still alive, Hypatia's flesh was torn off using oyster shells. This is notable, because John of Nikiu also portrays Hypatia as a witch:
The punishment of witchraft had been determined decades earlier by Emperor Constantius[?], as noted in Soldan's and Heppe's Geschichte der Hexenprozesse [3, p.82]:
With no iron hooks available, Hypatia's death seems to match the prescribed punishment for witchraft precisely. She may have been the first famous "witch", as was noted by many church-critical authors. In spite of Cyril's involvement in her murder, he was later declared a saint.
Some authors have used Hypatia's death as a symbol of the repression of reasoned paganism by irrational religion. Included among these authors was the astronomer Carl Sagan, who provided a vivid account of her death and the burning of the Library of Alexandria in his popular science book Cosmos. Earlier writers with that perspective include Voltaire and historian Edward Gibbon. A recent work by the Polish historian Maria Dzielska explains Hypatia's death as the result of a struggle between two Christian factions, the moderate Orestes, supported by Hypatia, and the more rigid Cyril.
 Letter 154 of Synesius of Cyrene to Hypatia (online version (http://www.geocities.com/hckarlso/sletter154)).
 John, Bishop of Nikiu: The Life of Hypatia. Chronicle 84.87-103 (online version (http://www.cosmopolis.com/alexandria/hypatia-bio-john)).
 Soldan, W.G. und Heppe, H., Geschichte der Hexenprozesse, Essen 1990. (English translation by Erik Möller.)
A global movement promoting the freedom of knowledge and free software was founded in 2001 to honour Hypatia of Alexandria. (Read The Hipatia Manifesto (http://www.hipatia.info/index_en.php))