You have a raised a very tough but good question! This is a common fear that parents of spectrum kids have. Middle school, as we all know, is cruel to everyone, and especially to those who are different. How do you let your kid be who they are while still protecting them so they don't emerge traumatized?
I feel what is most important is not to let your kid feel ashamed of who they are. If they've got a spark to them, they've got things they're interested in, don't kill it by making them conform. Most people lose that spark naturally when they get older; there's no reason to do it prematurely. Don't take away one of best things your Aspie has going for herself: her passion for living life, even if it's living life on her own terms. If she wants to fit in, she'll ask you how to fit . It'll come, but let it be when she's ready for it rather than force her into a cookie cutter existence.
Some Aspies go through middle school so excited about their passions that they barely notice they're the odd ones out, or if they notice, they don't care. Probably not a lot, but some. Others are unfortunately bullied quite a bit. There are a few things you can do to try to either prevent this from happening or minimize the effects if it does. First, use her talents and passions to find her a niche in the school where she can succeed. The drama club is a natural place. Many quirky kids find refuge in drama clubs; and if she can succeed in school plays, then she has one place where she belongs and can be accorded respect. If there's a particular subject she's interested in, see if she can start a club and find other kids interested in the same thing. Or find if you can a group outside of school interested in that kind of thing. Buffer her so if she does encounter some rejection she will already belong to and have found success in enough other activities that it won't really matter so much. Perhaps you could encourage her to take interest in a particular teacher, especially in a subject she enjoys, so she could have an ally at the school. Teachers were always invaluable support people to me when I was in school.
If she does encounter problems, try to find ways around some of the biggest trouble spots. For example, she could eat lunch in a classroom instead of the lunchroom if the lunchroom is problematic. If bullying does occur, hopefully you can work with her and the school to minimize the amount of places that it occurs. Keep reminding her of how great she is, and let her cry to you if she needs to. But the most important thing you can do, it seems, is continue to let her be who she is because it's not worth losing yourself for a bunch of junior high kids, and give her outlets where she can succeed so she's not as bothered by the junior high kids. Also, if she's into it and they're available, a support group for Aspie teens may be valuable.
I wish you the best while traveling this difficult journey.