Yes, one of the issues around aural plaques is that treatments can be painful and the horse develops a real aversion to having his ears touched so it becomes more and more difficult to treat. Some desensitization can be useful, but given the severity of this case, it is going to be a long road, and this horse is going to have having her ears touched. If I were you, I'd reward the horse each time you treat it by giving a favorite food. Even then, it may become harder and harder to treat.
If the horse is being ridden, you'll find it difficult to get a bridle over the ears. I'd avoid rubbing against the ears at any cost right now since this is going to be painful for quite some time. Halters need to be unbuckled and re-buckled so the poll piece can be gently be placed over the head. I use a bridle that can also be undone so I don't have to pull it over his ears. I put in the bit, and wrap it over his poll, buckling it at the side. The brow band comes off and snaps back on after the headstall piece (the part that attaches to the bit) is on. It looks like this: