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?

Local forces, which includes not only PDF but obviously also any rebels that would arise on a given world, sport weapons and vehicles that may well be different from the IG standard, unless the world in question is supplying the IG (and even then they likely would not have everything ). Autoguns and -pistols are obvious weapons of choice, with ammunition being produced and sold locally rather than having to be shipped into the warzone over a distance of several thousand light years. Even the tanks would be different, as you already mentioned. Insurgents would probably make use of converted civilian vehicles as well. I've just read the short comic "Pax Imperium" which was about the last stand of an Arbites Precinct House, and there the rebels used a giant tractor (as in: really huge, a bit larger than a combine harvester) to break through its reinforced doors.

Personally, I'd not have rebels have a sort of "Commissar", unless we're talking about evil guys who want to dominate their forces through intimidation rather than conviction. Not having a Commissar is one of the amenities of life you get to have from not living under the Imperium's rule, after all. If you want to have "Browncoats" who truly believe in their cause, a charismatic officer is more than enough … and certainly more suitable to challenge your players' own perception of the universe!

The 3E Witch Hunter Codex also had an Adversaries section which included stuff like Apostate Cardinals, Traitor IG and Mutant Rebels, if that's of any help.

You need to choose/clarify whether you are looking for freedom fighters who actually have a legitimate cause, or for corrupted/subverted traitors in liege with Chaos. There would be a notable difference between the forces and weapons the two would field, as well as in how this might possibly affect your players!