I hope the meds sort Kali out and it proves to be nothing more than an infection.
I am actually pleased that your vet is taking it seriously though, as so many times I've seen dogs with something wrong going back and forth to the vets and then eventually after months of various medications, finally being sedated and x-rayed. If it is my dog, i much prefer them to be completely checked over to rule out the serious things first before concentrating on finding out what it really is.
I'm not even going to tell you not to worry, as it is impossible not to, but the vet has said that she is putting on weight, so it is more likely that the hole in her palate is causing her a problem.