I have drove miniature horses and standardbred race horses for a long time. Horses may not ever be able to see the whip in harness, but the know when that whip is picked up out of the holder. I teach all my driving horses to go off of clucking or voice commands and we just leave the whip in the holder for decoration. I have drove other peoples miniatures though who do use whips to get them to pick up the pace and I know when that whip was picked up from the holder, most of the horses were moving a whole lot faster without even being touched because they had heard the noise of it being picked up and associated it with being smacked with it before. So it may not be a problem with seeing a whip but maybe just that she associates any noise behind or beside her being a whip. As was said before, some desensitizing and she should be doing just fine.
You know how to make a miniature horse even smaller? Leave them in the dryer a little longer!
"Don't ever regret something that once made you smile"