Haven't finished it yet but I thought I would post my one criticism of the Arroway character and how I read the priest scene.
Ultimately, Arroway's transformation into an atheist appears to be due to the death of her parents. Because the priest says it's all god's plan, it essentially blames this god for her loss and thus her subsequent rejection of belief appears to stem from a rejection of god.
I've often encountered theists who claim that atheists hate god and deny him. That she is in large part an atheist because she was orphaned by 'god's will' affirms this Christian attitude and even when the film does present her beliefs as being based on reason and logic, the audience is left remembering that the process started with 'god took away my parents'.
There's also that awful emotional argument from Palmer Joss - "Did you love your father? Prove it." She should have slapped him.