As scary is this is, it is actually BETTER to breastfeed when you are both sick. Breastmilk will help boost her immune system, and you will actually pass on many of your own antibodies that your body is producing in response to being sick. Most illnesses are not passed on through breastmilk, and usually only ariborne or passed on through physical contact. The best thing you can do for both of you is to drink a lot of water, and breastfeed as often as you both desire.
Your C section site is probably sore because your abdominal muscles are being strained by the diarrhea. While an allergy is possible (I became allergic to apples after giving birth to my son), with your fever it is more likely to be viral.
If your doc says it is ok, you can give her infant tylenol to make her more comfortable. Also, clean her bottom with UNSCENTED aloe wipes, and powder her bottom with cornstarch. It will neutralize any remaining acid and dry up the bottom without irritating it. It is also safer than talc.
Unless she gets a high fever or either of you get dehydrated, you should both come out of this fine.