Another idea could be that Atlantis is still on Earth (perhaps permanently). Thereby not having a need for 2 stargates (since one would always be primary), perhaps the SGC was closed down, and the IOA elected to make the Atlantis base the new base of operations for all things related to the Stargate. General O'Neill as far as I know is still in charge of Homeworld Security (unofficial name ofcourse), and this department is likely housed at the Pentagon.
One could argue though, that Atlantis would have to be permanently cloaked for this to make sense. It did land failrly close near the Golden Gate Bridge so it would be hard to otherwise miss it.
Its more likely that all stargate-related operations are based at the Pentagon. Maybe even Earths stargate is there somewhere. It would be good for plausible deniability.
There are 2 things, maybe 3, that could have happened with Atlantis:
1. It is still floating near San Fransisco, while cloaked.
2. Somehow, power was restored for a limited time, enableing someone to be able to fly Atlantis somewhere temporally, possibly the moon, with its shields up, untill full power can be restored in order to send it back to the Pegasus Galaxy.
or
3. Full power was somehow restored already and the 'wormhole drive (SG translation of Deus Ex Machina, lol
)' was used to send Atlantis back to Pegasus quickly.
Point is, it makes more sense to have all stargate-related operations continue from the Pentagon.
