That is where this film went astray. Had it concentrated on those aspects, it would have been a much better film. The Bishop actually defended Hypatia in real life. And she was, as you mention, neoplatonist not atheist. She actually found value in Christianity as much as her other influences.
Interestingly, one of the early church scholars who preserved the churches reverence for her knowledge was socrates scholastica. I have already drafted a post for Easter that quotes him on the whole revisionist "Easter is a pagan holiday" lie that gets spread this time of year.