Go see a lactation consultant. The pain could be normal or it could be something else. But what I'd really want to know is if your baby should have been treated, too - with thrush, both mom and baby need to be treated even if only one has symptoms b/c they can keep transferring back to each other. I'd be concerned of something similar with staph.
As for drugs and nursing, the antibiotics should be safe for your baby. Remember that if excreted in breastmilk at all, it's generally just 1-2% of the original dosage, and that babies are prescibed antiobiotics, too. So if you are nursing while taking antibiotics that have been ok's by your dr/pharmacist for nursing, there's no need to limit her feedings. That could also seriously affect your milk supply.