The way I see it, the Wraith no longer pose a direct to Earth. None of their ships know Earth's location, and aren't capable to travelling to other galaxies regardless. The Stargate in Atlantis itself was the only one in Pegasus capable of dialling Earth. It may seem cruel to the humans living in Pegasus, but keeping Atlantis on Earth is by far the most logical course of action.
Although, they could always send the entire fleet of Asgard-enhanced BC-304s to the Pegasus galaxy and make short work of the Wraith.
EDIT TO ADD: I remember a few weeks back, someone here had a thread noting the SGC hadn't been featured yet in SGU, save for Daniel's video. In this thread it was speculated that the SGC had moved out of Cheyenne Mountain and relocated in Atlantis. If you'll note, in Air we see both Walter and Dr. Lee working at the Pentagon now. Dr. Lee isn't so shocking, given we saw him assigned to the Midway station. But Walter has been with the SGC since the beginning. If he's no longer there, it could be because it really has shut down, and he didn't transfer to Atlantis because Chuck already handles the gate dialling procedures. Something to think about.