Without taking away from the "domain swipe" that Jonathan has pointed out (good find) it's not a clear cut case of "big brother taking a domain name" like a few of the State cases in the U.S.
I am quite sure that the FBI has substantial evidence supporting their case as James pointed out (great find) regarding charges. The domain name was an asset in the ability to commit the alleged criminal acts and therefore can be just like a bank account or any other asset acquired by the charged parties involved.
If found innocent, then the U.S. Gov would have a MASSIVE debt about the size of the one that Obama is currently putting them under with the spend he's put on since in office after having to pay damages to the websites for lost revenue and potential earnings etc.