of ALL the books I have read, and speaking to doctors and lactation consultant, they all say it is OK to breast feed the baby while you are sick (with a flu, others, I can't say for sure). What kind of medication your doctor gave you? It should be mild enough that it won't harm your baby. In fact, by the time you build up your antibodies, your baby will acquire that as well, which is good for the baby!
dear annie: if you pump after you feed, may be that is why there isn't as much as you think! As long as the baby keep sucking, I believe our breast never runs run out, it is a matter of how much patience and provided the latching technique is correct.