One solution to this is to simply make it mildly unpalatable to play one of the "blending-in" Pirates in the first place.
Rogues and Bundschuh (yes, selfish plug) have the right idea by rephacking Pirate-IDed ships to No-Dock.
And honestly I don't think this is as big of a problem as it seems, regarding the "sit in front of a LNS-ship" thing. Liberty (in your example) outlaws a lot of the ships that potential Libertonian pirates might want to use anyway. It can still be presumed that a Pirate IDed Greyhound is in fact a pirate just by the colors he flies. Same with a Pirate ID-ed Bayonet, Arbeiter, etc.
That essentially restricts the in-plain-sight pirate to either Civilian or Border Worlds technology. And all I've heard about regarding those lines is whining about "RIP EAGLE" or how the Sabre is no longer the most overpowered ship in Sirius.
