I have used Baytril extensively with my Egyptians when they have developed a respitory infection. I am somewhat aware of the problems that can develop by the injections, however I have never experienced the problems myself. I believe the vets call this problem "sluffing of the skin" or "necropolis". (Correct me if I'm wrong on this EJ) Keepers should also know that there is a small animal Baytril and a large animal Baytril. I recently used the large animal type on my 13 pund Sulcata with great results.
I have found it difficult if not impossible with most of my tortoises (small and big) to give Baytil orally. Some tortoises allow manipulation for this, some are too strong. Many of mine are just too small.
Set the possible side effects aside that are mentioned above, what is more detremental to the tortoise? 15-20 mins of trying to give Baytril orally by poking, pulling, and prodding it, or a 5 second shot in the meaty portion of it's arm. This really is a question on that point. I am inclined to think the tortoise is more stressed by trying to force something into it's mouth, but I am open to being enlightened on this.
For what it's worth...
Tortuga