I've definitely been where she is.
My family was SUPER fundamentalist too. And it took me years and years to see through it. I'm still a Christian, and I'm glad to hear that you've found faith in God.
The thing I'd tell you is to be extremely patient with her, if you do decide to try and talk to her again. She'll probably say stuff that doesn't make sense to you, but you have to understand that someone has presented her with logic that to her seems inarguable. Someone probably told her that you were encouraging her to listen to false prophets or something since you were showing her how to look beyond just the bible for answers, that you were a bad influence, and that she should no longer see you. When I was in that church situation, I was told that the bible said not to be unequally yoked, so that meant I was not only not to marry anyone who wasn't a Christian, but that that person had to also be on a similar spiritual track and "level of spiritual maturity" as me. Whatever that means. But it basically excluded the whole world, except the 5 or so men within 10 years of my age at our church. So don't take it personally too quickly.
You've been an atheist, as you mentioned, so I'm sure you've seen the ridicule fundamentalist Christians are exposed to. It looks so crazy to someone on the outside that they can't imagine how stupid you must be to have been so duped and controlled. "Don't they think for themselves at all?" they ask. But in reality it's not very hard to believe it when you're stuck in the middle of it, and with seemingly infallible logic that the leaders claim comes straight from God how can a person argue? It's legalism, something that the people reading the bible always seem to add to it without fail, and it'll get you.
This is an issue near and dear to my heart, and I could rant about it for hours. I hope all my rambling has helped you a little. Good luck, and I hope you'll let us know how it works out! :) I'd be happy to talk to you more about it if you want.
Best wishes,
Samantha