I'm traveling this same flight at the end of September with a wife who is a very anxious traveler. I'm keeping an eye on other options, specifically the JNB-JFK flight - but I, too think that the fears are irrational. The risk, from everything I have read, is de minimis. Remember - there is one confirmed case in a country of 14million. I'd take those odds any day.

Our compromise is to just be abundantly cautious - use anti-microbial wipes, purell, etc. She may talk me into some other irrational precautions but if it helps alleviate concerns it may be worth it.