Hello Sean,
I don’t know of a Rabbi who has experience with autistic kids because I haven’t had those sorts of questions.
It seems that your wife’s past sensory issues are not interfering with her dressing in religiously appropriate ways today. It’s possible that allowing your daughter to wear pants now will not preclude her from wearing skirts and dresses when she is older. Of course I’m not a Rabbi, but it seems to me that if she takes a little longer to “move forward” in terms of her dress this is not at all the same as moving backward. Just as your daughter may need more time to get used to different textures, sounds, and other experiences than do other children, she may also need more time to become accustomed to wearing skirts/ dresses.