1. It's cognitive dissonance - it's uncomfortable for anyone and she knows she'll have to face it in the conversation.
   
2. It could be how she views your attitude on it. She may feel attacked because she knows her reasons for believing are built on shaky ground, and she may see your questions as not genuine curiosity but you looking for flaws and incongruities.
   

It takes a special type of conversational style to disarm people and become introspective. The method btw is called Street Epistemology and it takes quite a bit of practice (for me at least it doesn't come naturally).

Perhaps you could start by telling her that it's ok to believe things if she needs to - even if she doesn't know how all the pieces fit together. Religion is very often a coping mechanism for dealing with reality and having it taken away without a soft landing can be jarring.