Ya know I'm a Linux user myself and cannot see the big deal with all this. The guy screwed up, committed a couple of felonies and agreed for his internet usage to be monitored.
As for the US government not having monitoring software for Linux: Is that really a surprise? Huge software developers don't support Linux, haven't for a long time and probably never will.. You honestly expected our technically inept government to hack Linux?
It's not like their forcing the guy to use Windows, just don't use the computer if it's so much of a problem for you. The biggest FOSS apps for Linux have windows ports anyhow, what's the big deal?