Well, that was fast.
Yesterday, American Atheists President Dave Silverman tweeted this:

Terry Firma gave more details on what happened on this site earlier today.
Today, Silverman posted his letter to appeal the decision on AA’s website.
And just moments ago, he tweeted this:
MVC caves – Will allow ATHE1ST plate! Stand by for statement!
— David Silverman (@MrAtheistPants) August 28, 2013
***Update*** (3:38p): American Atheists has released a statement regarding this controversy:
A reporter early Wednesday afternoon contacted Silverman to tell him that his application had been approved, and soon afterward a spokesperson from the Commission called to confirm it.
Once he receives the plates, Silverman plans to bring one with him to American Atheists’ 2014 National Convention in Salt Lake City, where American Atheists members will be able to take pictures with it.
Only at an atheist convention…