Definitely sounds like the infection has not reached a severe level and that is a plus. Not knowing the exact history, and going from your description, it sounds like there is a possibility that there may be a tooth issue going on here. This could be causing more of an irritation, and possibly not that serious of an infection. That is just a guess, and the vet would need to check on that.
Baytril can be given orally, but Cipro does not have an injectable form that I am aware of (except I.V. hospital use). Could the injectable have been something different? Both are fluoroquinolone class antibiotics and very similar in molecular structure, with Cipro being slightly superior in spectrum of activity. There are several other choices if it comes down to needing alternatives if the Cipro is ineffective in resolving any existing infection. There are two cephalosporin class antibiotics that have worked well in these cases. One is ceftazidime (Fortaz) and the other is ceftriaxone (Rocephin). The superior one is probably ceftriaxone, as I have seen it resolve stomatitis in snakes that was so severe it looked to be beyond treatment. Both are typically dosed at 20 mg/kg at 48 hour intervals. Another alternative is amikacin, but this one is toxic and more care is needed with it’s use. It is however an excellent antibiotic for the treatment of stomatitis, and can be used safely.
As always, the use of any antibiotic treatment should be under consultation from a vet, as well as the dosage requirements. Be sure to let us know how it turns out.
Kelly