Very true, ammonia burns turn brown/black when healing. Just keep testing your water and making sure that the ammonia level in the tank is 0ppm.
Is your tank new? What are the params right now?
You could add some MelaFix to help heal the fish, but if you keep the water really good, you shouldn't really need it.
About the pain, I never really thought about this before, but I am sure that it is not the most pleasant thing in the world for the fish

As far as I know, there is nothing you could really do to ease the pain...