1) Hurricanes are actually harmless to planes. The only part of the flight that includes any danger is landing, due to wind and low visibility. But flying at cruising altitude or even through the storm is fairly harmless, as most winds are horizontal and nothing out of the ordinary for a plane. Keep in mind that the NOAA regularly flies commercial jets (such as a Gulfstream V) into hurricanes. Also keep in mind that never in the history of aviation has a plane been brought down by a cyclone. Thunderstorms, on the other hand, are much more dangerous. The main difference is that in a cyclone, air moves horizontally, while in a thunderstorm it moves vertically in bursts, which is much more difficult to navigate.
2) From what I've heard, this was not a commercial flight but a flight mainly aimed at evacuating non-rev airline employees. The main issue with doing this flight for regular passengers would be fear and discomfort due to turbulence. Airline employees on the other hand are used to flying, know that turbulence is harmless, and would rather just get home.