Dealing with the arcade nature of ED. Shouldn't have happened, but it has become more arcade than sim. Sad really considering the sim part is what made it a historic game in the first place for all the nerds of the past. All you can do is do what all those are saying........learn to deal with it. Sucks but you got to. Even when out mining LYs away from the nearest sign of life, the NPC pirate shows up magically. Deal with it. Then you can get over it, and enjoy the game once again.
OPs story sounds like a good change from the standard. Which means FD is gaining progress. I've seen it recently with NPC encounters, and even if it has to be the arcade pattern of no matter where you are they will show up, as long as FD does it in a manner that doesn't turn the player away they have done it correctly. And that is what we want, or should want.