Hey LQ,
I found one particular part of your conversation with her interesting. I have heard it several times. I think the way you respond to the thinking is key. When she says "Do you think you are smarter than the GB?", you said of course not. But this is not really about intelligence. From her perspective (and maybe yours depending on what you currently believe about the bible), its about truth. Truth wherever it leads.
Just continue to show her love, and to do what you think is right. Try to discuss things on your terms, and if she comes at you ina huff try to defer the conversation. It will NEVER end well if it already starts heated.