if this is about sex before marriage - my advice to you is respect her wishes calmly and patiently.
if its shall we say more borderline - id advice you to get her to talk to her preist, about what they feel is appropriate behaviour in a modern relationship between 2 17year olds who obviously care enough about each other to be asking for help.
for any one to cry when they pray its is obvious that they truly do have faith, and trust me as she gets older that faith should mellow with life experience.
Id also suggest you go to her church with her, show her family and comunity that you are a part of her life and support her choices, feel free to explain that you dont beleive but say because you love her its important to you to meet them and understand her faith.
If she realy is as afraid as you put it id recomend buying her some presents - gifts of affection as it were. namely books about various faiths and history. your both quite young still and education as other have said is a great way to open minds.
I apreciate that your trying to help her but i think that the solution may lie with you, and your ability to accept her choices.
My advice can be simplified as this: accept her for what she is, dont try to change the person you fell in love with but theres no harm in learning more about a subject and participation in the comunity of your girlfriend will help assuage her fears.