Perhaps calling the fleets a name based on the faction they are drawn from might be better. i.e. Rebel Rogue Drones, Rebel Freedom Fighters, Rebel Corporate Dissenters.
I think that's a fine way to deal with it. And yes I understand that I am nitpicking a naming convention in a mod for a game that's in alpha... but hey, why not? It's only because I love the game and I love this mod.
Some ideas:
Heretic Fleet - Kadur
Extremist Fleet - Qamar
Rogue A.I. Fleet - Bushi
Corrupted Hive Fleet - Zorg
Renegade Fleet - Junk Pirates (or... Junkzerker Fleet?)
Zombie Fleet - Pirates.... obviously.
Insurgent, Separatist, Dissident... I think giving each Faction it's own flavor of 'Rebel' would add a lot of... uh...
flavor... to the game. Personally, I don't think they all need to say 'Rebel' in the name for people to quickly figure out that they can kill those guys without starting any wars. The bright yellow icon and the fact that they are 'hostile' and attacking everything in sight should be clue enough.
You could ask the creators of the Faction mods if they have a particular lore-friendly name they'd like to have their default 'rebels' labelled.
Oh and yeah... lore wise the Qamar
are the Kadur 'rebels' right? But since they are 2 separate factions, they'd both need their own internal 'rebels' as well.
EDIT: Side note... I think killing 'rebels' in another faction's territory should raise your standing with that faction some. Or does it do that already?