I think I will just point out that, for my money, these two interpretations are basically the same, with pagans coming down on the side of reason. Sorry, early Christianity--but pagans DID invent or discover most of what we're still using today toward scientific and rational ends.
I liked the movie, though I found it sort of uneven and oddly paced. People who know more about the topic than me note that the facts of Hypatia's story are up for debate, and that Amenabar takes liberties. But these issues are not really important; the significant bits of the film, which is to say most of it, are there and gleaming and horrifying and true. Still true. Religious groups clashing in violence in the name of their god (s)? CHECK! Religious groups clashing with "secular" governments in violence in the name of their god (s)? CHECK! Religious groups clashing with scientists in violence in the name of their god (s)? CHECK CHECK CHECK! No one comes off looking good in this story except perhaps Hypatia herself--the Jewish, Christian, and Roman-Egyptian pagans all do terrible things to one another: an eye for an eye is the rule of the day in ancient Alexandria.
Of course that is still true, too. It is still true that reactionary groups in my country and other countries care little about facts or scientific data and have no care at all for history. It is still true that pagan and indigenous religions are repressed, vilifed, and distrusted by mainstream religious groups, and scorned by secular ones. My, that was a lot of links! And there are far too many more instances of such events and language. Not much has changed from ancient times, it seems.
Beyond these themes, Agora also shows just how far we've come with regard to women in the public eye, women as instructors of men, women who are unmarried, and women with power. Hypatia is all of these things--a famed and respected philosopher and scientist, an instructor of male students, an unmarried, presumed virgin who publically rejects a male suitor, and a reasonably powerful voice in the agora and schools. At the film's outset she is at the height of her power, teaching science and astronomy to her students, defending the public peace with her voice, and speaking out for all religions. At the movie's climax, she is murdered by a mob, after being accused of witchcraft and seducing the Prefect--accusations backed up by the Christian leader's reading of certain passages from Paul. She is stripped by the mob--as ever men use women's bodies against them--called whore and witch. Hypatia represents for modern feminists an extant struggle: women in the workplace. Often blamed for not being assertive enough, for being too assertive, or for being too pretty, the fact of the matter is that in the United States, women in their workplaces still face plenty of discrimination and wage disparity and few laurels. Again, not much has changed.
And even beyond this, a topic very dear to my mind, Agora hit me one more time: the scene inside the Serapeum when the Christian mob sacks the library. A bit of history--the Serapeum or temple of Serapis hosted a portion of the legendary Library of Alexandria; it is not known how many texts were housed in the Serapeum. This temple, as well as Alexandria's other pagan sites, were sacked in 391 by order of Theophilus, the bishop of the city. In Agora, the Serapeum is sacked by the Christian group in order to get at the pagans barricaded inside. Regardless of historicity, this scene, as well as following scenes which show the destruction of the city's historical and cultural sites and the use of the Serapeum as a stable for animals, was totally shattering to me. That was the point when the tears started. As a librarian today, I see that this destruction is still going on, maybe not physically and with such violence, but the lack of care for preserving history and culture, for teaching and learning, is starkly evident in the US. Libraries all over the country are suffering, some, like the Camden, New Jersey system are closing all locations. For whatever reason, despite public libraries' intense usefulness, they are perennially on the top of the cut list when it's time to slash budgets.
Bottom line: Agora is a beautiful, provocative film. Just be prepared to be very depressed afterward.