I understand. We don't want to hurt our cats, and we don't want to damage their trust in us. You've worked so hard to gain Zidi's trust.
Remember how loose a cat's skin is. Think of how rough cats play. Their skin is tougher than ours by a good measure. Then think about the necessity that the mother cat must be able to move her kittens quickly and quietly. This has led to this physical reaction they have to scruffing. Kittens must stay still, silent, and in a posture that's easy to carry for the mother as she moves them to a safer den. Kittens in the wild that didn't do this were killed. Most cats retain this reaction into adulthood. Think about a mother cat's teeth. The kitten is hanging by her large front teeth.
I recommend scruffing with short nails, but I suspect that our nails won't hurt a cat even during scruffing. You shouldn't pick up an adult cat by their scruff, but you can pick them up with the other hand as you scruff them. You might need to use gloves at first. If you do, get them used to the gloves first. I was fortunate with Ziggy--he has no adverse reaction to gloves at all. He must have been handled with gloves before and he retained no ill feelings toward them. Use them to pet and groom the cat, and while feeding treats.
Harbor Supply has a good selection of leather welding gloves for $6-$10.
This will not work on all adult cats. Zidi may be one of these, but I'm not convinced yet. I wasn't sure I could scruff and clip Ziggy, but I did and it worked. Maybe practicing with Kilifi first would help to understand the reaction.
Try to scruff her when she is quiet and relaxed. Grab her firmly just behind the ears with a firm grip. If you have her held firmly in the right place, she should relax and even seem to become a bit catatonic--her eyes will often become unfocused and her body will take on a fetal position. However, this is the ideal. Often it takes a bit more, like it did with Ziggy. He saw it coming and was tense when I scruffed him. He tried to scratch and bite, but couldn't reach me. I laid him down on his left side and spent probably 10 minutes petting him, rubbing his nose, and acting like I was his mother washing his face--not with my tongue, my hands! He continued to try to bite, but he started to relax and finally relaxed on his side and let me slowly cut his nails. I'd do a bit and then stop and pet him.
Once you release them, cats seem to not remember the event. You can really tell when a cat is traumatized because they remember and actively avoid whatever they associate with the event. But with scruffing there seems to be some lapse in memory of the event during their "clipnosis", as Ohio State is calling it. They usually will get right up and act normal, as if it didn't happen. Even with all the work it took to relax Ziggy, he just stood up after I unclipped him and went on his way, with shorter nails.
I really do think it's the kindest way to handle the things we must do to keep them healthy.