Well if you read the warrant it seems the FBI are confessing BTC is considered currency. Although, I hardly think that this is the official stance of the United States government.
A judgment in favor of the US would be good long term for BTC under the principal of judicial estoppel.

Other that , this warrant is defective on multiple levels (like most warrants). There is no first hand knowledge . It doesn't even claim to have heard the information from someone with first hand knowledge.

Thirdly the Final rules concerning crypto-currency BTC were only just printed in the Federal Register.
The gov't is obligated to give MTGOX a notice to register their business because under he old rules they were not a money services business.

This is simply a money grab.