If he had done the deal in a foreign currency, in gold, or for modern art, they'd still seize all of that, regardless of its current value. Bitcoins are no different, even if you're considering them a proxy for real dollars.
As mentioned in the article, even after acquiring the wallet file, the FBI is still unable to perform transactions with that BTC. There's no bank they can order to transfer it into their account, no briefcase full of cash they can deposit, etc. As I understand it, the only way they're able to deprive Ulbricht of them is by not letting him keep a copy of the file. With the "brain wallet" strategy (not sure how viable that really is), they wouldn't even have been able to get this far.
Just from a redundancy standpoint you don't want one copy of your wallet in one location as it could get corrupted or destroyed in a disaster.
burying bitcoin can be done with a flowerpot.