Itraconazole is a great systemic antifungal, however it can cause GI upset in almost any species. It is certainly possible that this is the cause for your cham's regurgitation. Had she been regurgitating since starting this med, or did this begin to happen more recently? If it only just started happening, then something else may be more likely to be causing it. There are several other systemic anti-fungals, however all of the azoles seem to have about the same effects on the GI. Some of the other classes of antifungals have even worse side effects and thus probably should not be considered in her case.
Long-term use of any antibiotic can also change GI flora, even though baytril is one of the more easy abx on the GI tract. I think your vet was probably reluctant to stop the meds because it sounds like they are improving her condition and your vet is probably worried that if you stop administering them, she may worsen, perhaps beyond the point of fixing.
A lot of the things we use to treat our animals with have both pro and cons. It becomes a matter of taking what has the potential for the best outcome. As your vet eluded to, if your chameleon begins to loose weight, then something absolutely needs to change. At that point weight loss and poor nutrition would be worse than the risk of infection coming back worse than before or not resolving.