I think that you should seriously consider trying birth control pills, such as the Seasonale or Seasonique. If the side-effects of those are too difficult, you can also just try regular birth control pills and skip the "reminder" pills. That will give you the option of skipping just every other month or several in a row. If nothing else, the pills should make her periods shorter and lighter, which I'm sure would also make things a little easier.
If the side-effects of a specific type of birth control pill are too much, don't give up on the idea. Have her doctor switch her to another type. You could also look into the Depo-provera shot.
You may also try doing an internet search for "autism and periods" to see what other parents are doing who are going through the same thing you are. There are also books on teaching personal care to kids with autism that you might want to search for on one of the book-buying sites.
I hope you find something that works. Best of luck to you and your daughter.