Yes, the government could have seized the servers. But Carpathia and Cogent would have fought the forfeiture, and probably would have won. They were simply leasing server space to what they thought was a legitimate company. They can't be expected to be responsible for every file stored on their servers by their clients. That's like holding the bank responsible for what someone keeps in their safety deposit box. In the end it wasn't in the government's best interests to seize all of the servers and store them only to give them back later.
Instead they seized the data on some of the servers; most likely what they needed to prove their case. At the end of the trial they simply delete that data and never have to go through any forfeiture proceedings. The companies keep their equipment and can lease it to someone else.
In other words, it's nothing at all like pirating content.