FBI actually does what ever the hell they please, anything they cant do public they have mercenary agents for...
The article says that the guy was arrested by Garda Siochana, which is the Irish police.
So unless the Irish police are dumb (which is also a possibility), the coins stay with an Irish court.
Otherwise I foresee an interesting diplomatic issue arising very very soon.

Hopefully people reading the silkroad article and any other such news will remember the above and realize bitcoins themselves aren't bad.