If history is any indication it will be local police responding to shots fired. Many municipalities in NJ do not allow the discharge of a firearm within town limits. Morris Township has such a law in their code as well.
It would be like shooting someone for taking pictures of your house from the street.
I'm relatively certain law enforcement would have opinions about that.
If a drone is trying to gain access to your home, do you have the right to defend against it using deadly force? Meaning; Force that would be deadly to a human attacker.
That said, the FAA's jurisdiction ends with the National Airspace, which physically ends the moment it crosses into a structure.
There's plenty of states where you don't even have that.