Basically, I can see factions that rely on PvP getting PvP related perks, a capital vessel of their enemies, or something like that, which, usually need to be SRP'ed. Pirate factions, well, I don't really know what they can get from gaining perks. Maybe TLAGSnet access? Or a limited version of that? (though, it would cause so much tears on the forums)
Trading factions can be awarded, don't know if this can be implemented, a larger cargo hold ship, or something similar...one per faction. I can brainstorm a few more ideas, if I can guess properly. Or better, the faction leaders can ask what they need and the admins can verify it.
Though, yeah...this is a very welcome change-to-be.