You bring up an interesting point. There are situations like that in a lot of states. Georgia, for instance is a red state, but in the city of Atlanta you have a huge blue population.
I think that a dire economic collapse (which more than likely would be one of the forerunners of a civil war) would sort out that problem, as there would be a huge inner city population die-off from starvation and riots.
But also, in an old-style civil war, you might possibly have big states bully smaller states. MA wants to be blue. CT wants to be blue. If, by any chance, Rhode Island had any doubts, I think their bigger enighbors would just send them a memo: "You're blue." And the Blue Federation gets a little bigger and stronger.
But in a present-day civil war, it's not like that. Phildelphia wants to be Blue? Pittsburgh wants to be Blue? Well, how are they going to link up? They are both behind enemy lines. They are besieged. Supplies are not going to get through, and they cannot reinforce each other.
In an electoral system, large population centers can sway the results very effectively. In a military situation, the urban centers are practically dead on their feet at the very start.