The article title is misleading. The article says "this week, the FAA confirmed that that includes drones" without any attribution to any FAA official or FAA document that I can find. The content then refers to an April 2016 article in Forbes where it was stated that shooting at a drone would be a felony. What the FAA is stating at the moment is that the incident is being investigated.
I look at it this way, the law states that shooting at an aircraft is a federal felony, N.D. does not have anything on the books that would permit shooting at an aircraft, federal law supersedes state law, the cop/department will have to establish solid threat justification for shooting at the multirotor, and enforcement of airspace is not within the purview of local law enforcement. The owner of the multirotor likely has grounds to push for felony charges for several causes. Whether or not it's wise to do so is another story. He may simply just have a get out of jail free card. To not prosecute this event would establish a very dangerous precedent and broad Constitutional issues.