I spend a lot of time coaching young women to function in nearly all male environments.
I really like everything from Dude except the bit on having her change her own emotional response to situations. It's not a wise path to teach girls that their emotional instincts are wrong. I like the approach of teaching her to understand the boy's behavior and perspective, though. I like it a lot. This is similar in approach to what I coach my students to do.
The thing I would add to the approach would be to simply validate what she's feeling. It sounds like she's also feeling a need to remain loyal to a large number of friends and classmates, even as their educational setting continues to be in flux.
All that being said, this is a special education school. What does the school say? What are they doing to support your DD socially and emotionally? Surely these extremes in student population will be a constant part of the school's fabric, particularly considering the small numbers.
In parallel to all this, it is really useful to provide an all-female environment for girls in situations like this. Girl Scouts can be hit or miss, but a lot of the focus in older grades begins to be one of leadership. Learning to lead (=express herself effectively) in that safe atmosphere most certainly transfers to situations like these.
