Besides loading a previous save, no.
If you kill a member of a faction, that faction and their allies will hunt you down to the death unless you load a previous save from before you killed the guy.
That said, being hostile with the Protectorate doesn't lock you out of completing the game to my knowledge (so long as you didn't aggro any other major factions, like the Core City oligarchs, SGS, the Tchortists, etc.), but it will make certain quests extremely difficult or outright impossible to complete.
