This leads me to think that they are just trying to control the ways you put funds into and out of gox.
From reading the warrant and affidavit I understood it as follows - there is another corporation called Mutum Sigillum which seems to have been setup by Mt Gox to receive payments is the US from processors like Dwolla (who probably can't / don't / won't deposit to foreign accounts). When you send money to Mt Gox (for example) through Dwolla it was being sent to Mutum Sigillum's account in the US which then transfers the money to the Mt Gox account in Japan. In this capacity and under US law Mutum Sigillum was acting as a Money Transfer Agent which required them to comply with FinSEC. Unfortunately when Mutum Sigillum opened their bank account they specifically noted that they were not in the business of transfering money for clients. When the DHS realized what was happening they presented the evidence in court - the record of wire transfers between Mutum Sigillum and Mt Gox as well as evidence from an unnamed source who was able to purchase and transfer us funds into Mt Gox through Dwolla - and received a warrant which effectively froze that Mutum Sigillum US bank account. There is nothing to indicate that this had anything to do with Bitcoin specifically just the DHS attempting to enforce money laundering laws.
Although not relevant to the law I'm assuming that a significant amount of money must have been being transferred betweeen Mutum Sigillum and Mt Gox daily for the DHS to do something about it. There is still nothing preventing you (nor I image there will be in the foreseeable future) from going to your local US bank and sending a $100k USD wire transfer to Mt Gox. Of course the bank has to comply with FinSEC which means you can't make the transfer anonymously and it has to be reported to the government.