[1] As to whether the government is morally, ethically, or legally entitled to the seized properties, I have no opinion. I don't know anything about the situation.
These coins were technically owned by all the people with accounts on the Silk Road and were not necessarily going to be used for illegal transactions. For all we know this is basically government stolen money from some guy who wanted to buy a sandwich with Bitcoin just for the laughs and to say he did.
I think the money in GP refers to the other side of the trade -- if you sell an asset on an exchange, you are going to then have money (received from the purchaser) that is yours on that exchange until you are able to extract it.
Ideally, that would be trivial, but that hasn't always been the case for BTC exchanges (Mt.Gox being a notable example for an extended period of time.)