I'm so sorry to hear what you and your poor daughter are going through. I can't imagine how difficult it must be for both of you. One thing I wanted to ask - is she clenching when you administer the medicine? By clenching I mean tightening up her muscles. The more relaxed she can be, the less it will hurt. When I used rectal meds, I had to tell myself to slow my breathing and relax my rectal muscles. If you can explain to her that she has to be as relaxed and loose (muscle-wise) as she is when she's sleeping (give her that frame of reference), maybe that would work. It might even help to use some relaxation techniques before administering.
As for the prednisone, it may seem like an easy answer for the short-term but as many people on this site will tell you, you should avoid long-term use at all costs. And from what I've heard here, after your first use of prednisone, it often loses it's effectiveness.
As Sherry said, it can be terrible to watch your child suffer; but when you know you're doing it to ultimately make her feel better, you have to keep going.
I'm saying a prayer for you tonight. I hope her symptoms improve quickly, so you can both find some peace with this.
PS. I just had a thought. You mentioned you were using Cortifoam, and the times when I used it I noticed that although the tip was very narrow, it was very pointy. And if my aim was off a little, the tiniest poke really hurt. Maybe your doctor/pharmacist can give you another applicator that's rounder/softer.