I'm proud of you for letting her know your feelings! Definitely just let it take it's course and enjoy your friendship. In the future it may turn into something else, but honestly you have a lot of new things coming your way and in my experience these new experiences tend to change people. During the next few years, she may change as well (Not necessarily in a good or bad way, but everyone changes as they mature). When I was in HS I had a similar situation with a guy, except a bit reversed. We were the best of friends and did EVERYTHING together. I went off to college and he went to community college. The few times we got together after starting college, I realized he wasn't the same person I had liked in HS. The change we went through pushed us apart. However, I had one friend in HS who I was close to, but I wouldn't have called her a best friend. Now that she is done with college, and I think the experience really helped her mature. Now I would say she is probably one of my closer friends, and certainly one who I really enjoy hanging out with.
I guess what I really want to say is don't wait for anyone, even if there seems to be a slight possibility they may like you. This will cause you to miss out on other great opportunities with other great people. Who knows? You may find someone to be with on your mission! I would not suggest getting involved with someone before leaving for two years though. So many of my friends tried the long distance dating thing when they went off to college and hardly any relationships lasted. It caused a lot of stress for them, and the few relationships that did last just were not very happy ones.
Good luck though! Don't worry, you'll be alright. It's amazing how much a rejection can hurt, but at the same time it can really make a person stronger.