Ooh, that part actually works for me -- it seems very realistic, and it does not reflect well in the alliance.

As I see it, the alliance command is stuck with a political problem -- one of their best people has just committed a war crime. As far as they're concerned, the crime itself isn't a big deal -- batarians are The Enemy, after all -- but the political repurcussions could be huge. Still, Shepard gets things done (and in fact, some of alliance command might be happy about the dead batarians), so rather than get rid of her they give her an office job and/or put her on some version of house-arrest. It's not because she's useful there, it's because they're storing her for later, after all the political crap blows over. Out of sight, out of mind.

Basically, think of every time a police officer or important official has been accused of some awful crime, and instead of getting the works they're put on 'administrative leave' until people forget about 'em. THAT'S what I think they did to Shepard.

The brass doesn't care about her genocide. They just want to look like they do.