I'm assuming the Cemetery station is going to be open, so if at the Lincoln, you could just walk across the bridge and catch the blue line there. Probably avoid a lot of the crowd issues that way, too.
Tons of people walk across the Memorial Bridge and use that station. We used to park on the side of the road over there and walk to the Lincoln. We'd always see huge lines backed-up above ground trying to get down into the station. Foggy Bottom would probably be a better entry point, but I've never really witnessed what that station is like after the fireworks. Either way, you are boarding an already full train if you are headed toward Springfield. Trains headed back downtown would be empty and you could take that into town and over to Yellow and back out toward Eisenhower. I've never tried that, but that might be what I try if we go down this year.
Basically, you either have to wait it out, be ok with dealing with the mobs, or be willing to take a non-direct route and work your way around. My suggestion would be to find a restaurant, sit down for dessert/coffee/whatever, and wait it out if you really don't need to be anywhere.