I would not use hobbling as a tool to keep the horse still. It could put him into a panic mode since he is already nervous, then he can't get away from the scarey fly spray or hose. Hobbling can put both you and the horse in greater danger in a situation like this.
For now, why not wipe on the fly spray instead. Figure out where it bothers him the least. If there is no place he is comfortable with it, then fill a bottle with water and just spray it around regularly (not at himt though) whenever you are out in the barn, when you are leading him, when you are grooming him, etc. etc. Then spray over his butt, then his butt, then over his back, then his back and belly, then move on to the legs, then shoulders and chest. It may take a very long time to be able to spray his neck.
Be extremely careful not to get any on open cuts of course and around his face. If he already is scared, a bit of pain will put you two steps backwards with him.