My first forum post so please go easy. ;-)
These kind of FF situations have happened to me a couple of times in the past few months, but I'm getting steadily better at avoiding them now, e.g. I've learned to quickly roll my ship to prevent turreted target-only lasers having any line-of-sight when friendlies pass near my target (quicker than pressing a button to retract or switch-mode), and preventing myself from holding the cannon trigger continually when there's a risk a friendly could pass by. But generally speaking, whenever this happens, I know the current solution is balance to shields/engines, boost the heck out of the area, find a neutral/friendly station and pay my dues.
I still think there need to be some tweaks, but not having beta access, can't tell exactly how this will pan out in 1.3/PP yet. There have been so many posts on the subject, so its kind of difficult to work out exactly how the in-game logic works (before/after PP). i.e. FF on a green/friendly is not as bad as FF on a orange/neutral ship - as far as I can tell, that's how it appears to be now(?). If the situation becomes significantly harder with PP, and maybe players need to travel further or wait a week just to pay off a fine/bounty for an FF hit, I can imagine its going to get a little annoying, and its going to be a bit harder to recommend this game. I'm hoping FD find a balance because I'm really enjoying the game otherwise.
Last night though, I was playing solo, cruising around a nav beacon doing a bit of bounty hunting and after a short lull in fighting, I noticed that a couple of system defence friendlies started shooting at each other (FDL/Condas). I didn't join in as I was a bit low on ammo, but my scans revealed that the highest bounty among them was 400cr. The same ships were clean earlier on, so it appears that NPCs get punished for FF too. No idea how much their ammo and repair bills were, but I'm assuming they would be considerably more than 400cr - hardly enough to justify a fight to the death IMO!