How can a cat be given antibiotics other than by mouth?

We take care of a feral colony, and one of them, about 5 years old and a 9 on a scale of 10 in feralness, is a neutered male who was seen drooling and was finally captured and deflead, etc. The vet said he has stomatis but is not fiv positive. He wants us to give him a pill (Baytril) once a day but when you touch his mough area at all the entire mouth goes into something like a spasm as though he were biting very quickly. He is difficult to handle when trying to pill him, but he is ok with one of us scruffing him, the other clipping nails, or cleaning ears, etc. We wonder if there is some method like a daily shot instead of a daily pill to help this cat? And how dreadfully expensive would alternatives be, approx? He must have the antibiotics before he can have a dental and have teeth extracted. We will be contacting the vet, but it is not a very large practice and often we find that there were other ways to do things than the ways our vet offers. Any advice before we call is greatly appreciated!
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Baytril (Enroflaxacin) comes in an injectable form, but it is usually given either in the vein, or in a dose of fluids under the skin (because it stings when given alone). Baytril can also be given in the muscle (IM) but unless you are very medically savy, your vet might not want you to do this. On the other hand Cephalosporin (Cefa) is commonly given as an injection under the skin (just like you would give insulin) it is another antibiotic that is sometimes used on feral cats or when Baytril is not working. They also have some antibiotics in transdermal gels. The medicine gets absorbed through the skin. You put a small amount of gel on the ears (usually 0.1 mL). I know for a fact that Zythromax (Azythromyicin) comes in a transdermal form. Since you said your vet was small you can ask your vet to write you a prescription to be filled at another vet or by an online pharmacy (Roadrunner is where we get all of our transdermal gels- they will deliver to your home). As far as expense goes, Baytril is one of the most expensive antibiotics for cats, so there should not be to much of a difference. The transdermal gels are expensive but again, it varies on where you live and what vet you go to. Last but not least, Baytril is liver flavored, you might be able to get away with mashing it up and mixing it into a small amount of wet food. Find the smelliest, stinkiest wet food that you can and try mixing it into it. On most cats you can get away with one tablet (22.7mg) crushed up into two - three tablespoons of canned cat food (or Gerber 2nd Step Chicken and Gravy Baby Food-- Cats love this, it is what we feed sick cats that won't eat). Best of luck
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