There is no single command that can correct reputations as far as we know, the new faction relation (system?) is very complicated - even if its only using Global variables to keep the faction scores. I suspect these are held in some kind of list like a Leveled List in which each faction has a score for the player. When we worked on Freelancer the faction scale was -100 to 100, with 0 being neutral and all messages to the player, combat interactions, etc were based on those scores. When the player moves it far-enough in one direction, we get a message about how that faction realtionship is going.
That said, there _may_ be a single console command that can set a single faction's score, and that would be a Great thing, but I have not seen it yet. Perhaps someone else knows of a way to do this already, but I don't know that anyone has decoded the new faction system just yet.
Miax