Here is a crazy thought. Maybe BurtW is behind bitmixer.io (or at least the government thinks he is behind it). I think running a bitcoin mixing service (some may call this a laundering service) could possibly fit the description of the allegation in the indictment.

BurtW did more or less publicly endorse bitmixer in their announcement thread and said that he had used them for 'a large amount' of bitcoin when they were only a few months old. He even said that he was considering to invest in them, and their minimum investment is 100 BTC.

BurtW was arrested on October 14, 2014, and bitmixer's forum auction bid was rejected by theymos without explination on December 7, 2014 (only 3 weeks later). This would fit a timeline of theymos getting some kind of subpoena asking for information about both the bitmixer.io account and the BurtW account, and if bitmixer.io was compromised as part of the arrest, it would fit the rough timeline that it would take for the government to take over the service and familiarize themselves with a good way to track all the coins that pass through it.

What does not match is the dates on the indictment (it says from April 2013, and bitmixer created a bitcointalk thread in January 2014), although it is possible that government thinks he was behind bitmixer + some other mixing service or + something else.

All this of course is speculation