The way I see it, there are only 2 logical options;
Please note: I'm aware you can't actually remove them, merely make them not sold
1; Remove all the Nomad ships, remove all or work at removing all of the non-FL ships
2; Keep the Nomad ships and make the ID/Tag available via admin approved request.
The reason is, if you are going to say Nomad ships are out of RP (despite being major canonicaly players in vanilla), you must logically apply these same standards to BSG/Homeworld/SW/etc ships.
You could potentially say that humanness is the only RP, but if you are going to go by in game avatars, you might as well say roleplaying Trent clones in thick jackets should be the only allowed RP. In any case, Star Wars Humans aren't even from Earth. They are from Coruscant. So they aren't human either.
Plus, the technological levels of different canons vary wildly. Homeworld is semi-hard sci fi about a notch below FL society in speed, but at Nomad level in production. Firefly is below FL in advancedness by nearly an order of magnitude. Battlestar Galactica is a close match for FL, plus it's story is semi reconciliable unless you consider the inconsistent and ridiculous extended intro to be canon (and if the Nomads could blow up a star so fast, why the hell didn't they blow up Minor either in the several months or more than 30 years between it's construction and the activation of the Hypergate/present.
Star Wars is completely and utterly beyond Freelancer in every way. There are 1024 SECTORS in their Galaxy, and the majority of their ships deliver petaton level firepower (for measurement, that's roughly 1 million times the entire worlds nuclear arsenal for a single petaton) in mere seconds and fly across the entire Galaxy using personal hyperdrives in merely half a day or so. They would be 2nd only to the Dom Kavash in power, and would actually make suitable RIVALS for the Dom Kavash.
Starfox.. well, that's a gray area.
Not to go off topic, but there's a species called the Kwa in Star Wars that, if we consider FL and SW to take place in the same universe, may have been the Dom Kavash. Read this; http://starwars.wikia.com/wiki/Kwa
So, we can either get rid of all the Nomad and non FL ships or keep them and make the ID/Tag available by request.