Well, the only thing we can really do is blast all of them to pieces. Not really much else to do about it. I'll keep an eye out from now on for whether or not smugglers are enemied to the Guard now, though. Never thought about that before.
Interestingly enough, I once managed to nearly get through the system in a Starflier, dodging fire and hoping like hell that they wouldn't manage to land more than one shot on me at once. Got to the jump hole to Major, and JUST as I hit the dock button I took a double-hit from a weapons platform. Blew me to little tiny Starflea bits. Admittedly I had a Mk VIII armour upgrade on that Starflier when I did that, but still...