I've always had good experiences using gc with eels and lions, really never an issue that I can remember, dozens of treatments. One important point, you must consider displacement. Her tank looks pretty bare so I didn't think to mention it, how many actually gallons of water is in her system? I have had issue treating other scorpion fish and I started splitting the dosage into 3rds, administering over 12 hrs, potency decreases pretty rapidly so you must get up to full dosage within 12hrs or so. Doing the water change is exactly what you should done.
So 3 main points, you treat actually water volume, and if concerned split dosage and ramp up. Maintain aeration, you can use airstone or just leave skimmer cup off if in the sump, or use a power head pointed to surface to break.
You reacted quickly and the time she was exposed should not be an issue in the long run, so hopefully all is well. Your point about the gills is not something I'm familiar with, but makes sense. And yes if the meds were clearing an issue it could also lead to stress. Rapid breathing is usually the danger sign to look for, unless an od without aeration, gc is probably the safest medication out there along with prazi pro.