"why it has been just fine for some guy to fly a drone above a tornado, but illegal, in the FAA's eyes, for a journalist to do the same. "
It is illegal for anyone without special permission to fly a drone over(sic) a tornado without a lot of special clearance. The "top" of a tornado will be well above the altitude limits on RC aircraft. It would also be in the realm of dangerous.
Flying over a disaster area is a different matter to take pictures is a different issue.
" A spokesperson for the FAA told me that the agency 'has proposed a civil penalty against an individual in New York City. The operator, who is a hobbyist, flew a drone carelessly or recklessly and violated air traffic rules as well. He ran the drone into a couple of buildings and it crash-landed 20 feet from a person (video).'""
And this is a good thing IMHO.