From what I've read the title seems appropriate. The agora was the open air marketplace of Greek cities where the merchants traded their wares. Obviously the movies creators are making a larger connection to the marketplace of ideas in which Hypatia works, and for which the great Library of Alexandria was meant to encourage. In contrast, it appears the early church, in the guise of the ironically titled Saint Cyril, will play the antagonist when his fanatical world-view brings them into conflict.
Although Hollywood is not typically known for documenting the life of the mind, what ever its merits, I look forward to seeing a depiction of the ancient world that concerns its self with ideas instead of battles, and the wrestling of conscience over the wrestling of armies.