Rebel scum. Innies. Browncoats. I just love these guys, as unlike many other enemies of the Imperium, they could threaten moral convictions of both player characters and players themselves. Unfortunately there is a danger, that they would seem a little bland, as opposed to, for example, fullblown Lost and Damned force or bunch of xenos, or even worse, they would be just Imperial Guard, but you now, the enemy.
Instead of giving them more or less "codex" (as in TT) equipment and unit equivalents (you know, seccesionist Leman Russ, seccesionist Stormtroopers), I would them them with more exotic stuff, Imperial Armours gave us ancient Malcador Heavy tanks, more towed artillery (by the why not use battlecanon in a way orks do, ie. as gun on wheels), Avrus Lighters remade as gunships, or worker strike forces and drugged up ogryns. Other good source could be Gaunts Ghosts novels, with heavy lasguns (laser machinguns), Usurper SPG (what I personaly image as earthshaker on Leman Russ chassis, so it could fit nicely with Thunderer and Tank Destroyer) or bunch of more primitive aircraft.
Rebels ought to have some commissariat equivalent, but it should differ from the Imperial one, be it more numerous and intented for combat as units (similiary to soviet NKVD and Interior forces), or make it more elite and esoteric (all-psykers, or conditioned such as envoys from Takeshi Kovacs novels)-There should definitely be lot of auxiliaries. Beastman volunteers, merceneries, allied chaos reavers and xenos, death-cult aiding the rebellion and such.
So, how would you make those guys unique?