Baytril may work but to be sure that you are killing the bacteria involved you need to have a culture/sensitivity test done of some of the "pus" or you might not be killing the germ.
If the bacteria has gone into the chameleon's system, then you are not going to kill it by only treating the mouth with a topical ointment and disinfectant. It will take an antibiotic too. You need to be very careful what disinfectant and strength of it you use or you could kill the chameleon....especially if it swallows much of it. The topical ointment needs to be one that will cause no harm if ingested, BTW.
A shotgun approach to killing parasites is not the best idea either. If a fecal isn't done, you might not even be killing all the parasites since any medications will only kill certain parasites. If the chameleon has a very heavy parasite load, you may kill the chameleon. Once the parasites inside the chameleon are killed they become waste and the chameleon's system may not be able to handle getting rid of that much waste all at once if the load is heavy.
Cleaning a small bit/area of mouth rot out without putting the chameleon out may be tolerable...but the pain/stress if the amount of "digging" you have to do is inhumane. The pain that they have to withstand AFTER the area has been cleaned out can be more than enough without having to withstand you doing it to them while they are "awake".