Ouch. If any of your other characters joined that faction as members (not just as Friends), and were promoted even once, you can recover this. That character just needs to use the terminal to "Claim Leadership" and wait 1 day, go back and Confirm that claim. He will be the new Leader there.
If this is not an option, then technically that faction is lost. The only way i know to fix this at that point is to patiently, humbly appeal to a dev's charity. But then again, it's so easy to build a fresh new faction, so maybe do that instead.