As Jersey says, Baytril is considered safe and many buns need to be on it long term, some even on life-long treatment. The side effects regarding cartilage etc is primarily seen with long-term use. Inappetence is the most common side effect, and if your bun won’t eat, you’ll need to syringe-feed, because nutrition is key when a bun is recovering.
Probiotics are considered useful for rabbits these days, because it’s nolonger just about lactobacteria (the type most used with humans but not found in the rabbit gut naturally. Lactobacteria don’t survive the very acid stomach environment). There is scientific evidence that live brewer’s yeast, saccharomyces cerevisiae, not only survives but is able to colonize the rabbit gut and helps poorly bunnies gain or retain weight.
Another type is called enterococcus faecium, it’s the most prevalent bacterial in the rabbit species and there is reason to believe that probiotics containing those can be beneficial for rabbits. Benebac has enterococcus faecium, but there are other brands as well.
It is recommended that you start a bun on probiotics while it’s on antibiotics and keep going for a couple of weeks after. Antibiotics kill off good bacteria and can allow bad bacteria already present in the gut in small amounts, to colonize the GI tract, if you give a good quality probiotic, the probiotic can out-compete the bad bacteria and prevent them from thriving . Enterococcus faecium has been shown to be able to do that in dogs and cats.
Sorry for being lenghty! I used to be able to link to a really great article about this, but unfortunately that site now requires membership login =/ You can register for free but the site caters to animal healthcare professionals: http://www.vettimes.co.uk/article/beneficial-bacteria-in-pet-rabbits/