Maybe I'm just stating the obvious but I think the biggest problem with player-owned stuff is the 3 different modes in which the game can be played.
If players own any kind of real-estate which is persistent within the game then somebody (or a group of somebodys) could locate that real-estate and then use Solo or Private-Group modes to do stuff to it and you'd have no way of preventing them..
Ever find one of those POI Outposts? Not the ones with data points to scan, but rather the ones that consist of something like A Large Building, or A Small Building, or even a couple buildings?
Ever try to do anything to them?
I've showered them in missiles, blasted them with Plasma, even emptied my cannons into them. And nothing happens. They're still standing.
The simple solution is:
Treat player "real-estate" the same way - It's Just There.
Perhaps a player landing pad could issue a loitering warning (no fine, but a warning) to any other ship along the lines of:
"Warning, this is a private facility. Clear the landing pad or face lethal response."
After the countdown, open fire with a couple beams like stations do. This should keep them clear of unwanted visitors.
Wanted visitors can park somewhere else.