After looking it up, the seizure wasn't related to the Silk Road case. It was because MtGox wasn't properly registered as a money transmitter and was operating their accounts in the US under false pretenses [1].
I don't think it's necessarily possible to link the Dowalla event to Silk Road directly (which was the FBI, not DHS).
At the time of the seizures that was the stated reason but later when officials were testifying before congress they implied that the enforcement against MtGox was related to the SR investigation. They hadn't moved on SR at the time so they were keeping quite about the scope of their full intentions.
What you linked to has nothing to do with SR or even congressional testimony. It's filling out the rest of their money-transmitter issues. First, they seized funds from Dowalla, and then from Wells Fargo. This was the WF seizure.
Seizing MtGox's USD funds may have had an effect on SR, but that wasn't the reason why they were seized. It was a money laundering issue, plain and simple. Remember, the funds were seized by DHS and the FBI was in charge of the SR case (which wasn't even against SR as an entity, but the owner/operator as a private citizen). I'm sure the FBI and DHS probably share data, but that would have required a lot of interagency cooperation for what is a pretty small matter. DHS was more concerned with blocking the money laundering possibilities than they were with blocking SR. Granted, DHS may have learned about MtGox from the DEA/FBI while they were investigating SR.
I wouldn't assume the gov't really cares that much about Bitcoin. They just want the players in Bitcoin to play by the existing rules.
I don't think it's necessarily possible to link the Dowalla event to Silk Road directly (which was the FBI, not DHS).
[1] http://techcrunch.com/2013/05/16/mt-gox-dwolla-account-money...