If I were in your shoes I would write her an e-mail saying that you had no idea you would offend her by choosing other bridesmaids, and that the last thing you would want to do is upset her because you've been so close, you care for her a lot, etc. Then explain that you are touched that she wants to be included in the wedding. While the wedding party has already been established, you would be honored for her to (do a reading? hold a candle? any other important role that hasn't been decided yet?)
Maybe if she feels included in some way--invited to shower, bachelorette party, even rehearsal dinner, even though she's out of town, that may help her feel less hurt.
In the end, I wouldn't add her to the wedding party, and it kinda sucks that she put you in this position. I think the most you can do is let her know that you never intended to hurt her feelings and that her exclusion from the wedding party doesn't mean you don't value her friendship.
Good luck!