Here's an idea that would probably be a pain to implement. If your entire civilization is overrun, you (the in-game leader of the civ) can escape to a non-hostile city of your choice. While in hiding, you can still control all of your spies (maybe the civ should get an extra spy or two). Then, if you're able to pull off a coup in a city state, you take control of the city state instead of simply gaining it as an ally. To make the strategy worthwhile, you could even add a new victory condition unique to this civ, where you win if you can regain control of your former capital after being overrun

Post Hitler Nazi Germany? Not a civ I expected to ever happen. Cool uniques though