I'm glad that you apologized to her later on! Good for you.
I've generally just avoided religious nuts as much as possible in my younger years because I wasn't equipped with the tools to deal with them effectively.
The biggest problem that I had when I was younger was that I didn't know that there was a word for my stance on religion until I was in high school. It wasn't until a girl I knew said the word "atheist" that I finally realized that there was a relevant word!
Religion wasn't really important in my childhood, but I wouldn't say that my parents were exactly atheists, either.
Yeah, it wasn't one of my proudest moments in retrospect. At the time, I thought I was in the right and didn't understand why I was sent to the principal's office. This happened when I was a sophomore I apologized to her in our senior year when I had a chance to mature more.
When in college I had a chance to actually meet the types of people who I railed against in my conservative christian youth (e.g. "liberals," homosexuals, atheists, etc) and I discovered that they weren't the "evil" despoilers of Western Civilization that my parents and right-wing squawk radio said they were.
It's no wonder why the religious nuts hate "secular" education Your outlook on life really can change when one is presented with facts that are not clouded by supersticion.