The US authorities seized the funds in Mutum Sigilum's Dwolla account because Mutum Sigilum was operating an unregistered money transmitter business. The registration requirements seek to prevent money laundering, but there was no evdience (at least that I'm aware of) that Mutum Sigilum was actually laundering money.
Mutum Sigilum was allegedly operating an unregistered money transmitting business, but there isn't much evidence of that either. The informant in the case only sent money back to himself. And even if Mutum Sigillum was operating a money transmitting business, it isn't clear that they are subject to the reporting requirements of section 5313 (which triggers the registration requirement) because such reports would be filed by Veridian and Wells Fargo.
The legal issues in this case are a lot more complex than you imply. If Mutum Sigillum was operating an unlicensed money transmitting business, then arguably Dwolla is too, since Dwolla is having Veridian transmit money for Dwolla's customers. You might also want to read:
http://k.lenz.name/LB/?p=9369