Beauracracy IS good at that. It just seems after the whole Arrival thing that making Shep a pencil pusher seems the strangest option. They pretty much let Shep get off easy considering the level of crime committed. If they wanted to keep an eye on Shep, then why not military jail? That would make the Alliance look better, and they could still get knowledge about the Reapers.

They felt Shep didn't deserve that, but still keep him/her working for the alliance, complete with uniform. It seems they didn't do anything with the info Shep has/gave them, so why keep Shep around as a walking testament to their failure? Maybe Anderson pulled some strings, but it just doesn't feel right within the context of the story.