J.W.
D., my 1-year-old daughter also has a g-button and I have used the silver nitrate sticks on her, too. She also fussed when I did it and not in the doctor's office. I would recommend someone hold your son very still while you CAREFULLY touch the granulation around the button in tiny little motions. It may take longer but the slower you go the better chance that you'll only touch the granulation and not the skin. You can't do it by yourself - make sure someone helps you and that the room is well-lit. Also, you might consider not using the gauze and just letting it air dry, which might feel cooler for your son.
I didn't have to do it that often and Sophie's granulation eventually went away. Don't beat yourself up about it (or the way that stupid doctor made you feel). Getting used to a g-tube takes time and practice. You're a great mommy!