Not necessarily. I mean, some of these independents are just examples from smaller factions. The ferengi, for example, would fit in perfectly and had decently armed ships.
I'd set up the ship categories for the independent faction as:
Freighters/Transports - the closest analog to the "cruiser," and start with lightly-armed ships similar to the tuffli, and progress up until things like the d'kora - still made for trade, but fully armed and ready for combat.
Explorers - Less heavily armed than cruisers/escorts, but relatively quick and agile. These would be the equivalent of science vessels.
Raiders/pirates - Just what it says on the box. There's marquis raiders, there's that ship from the TNG Gambit episodes, we know surplussed BoP's have ended up being sold at least a couple times. Basically small, fast crafts built for combat.
Possibly miscellaneous category like the klingon "warship" category for anything that doesn't fit with the above. There could be mining ships, scout/espionage ships, and anything else that's odd and doesn't quite fit.
"Stolen" is an option for VA. A great way for them to introduce a T5 Connie.
_________________ Nebula coffee is the best coffee