But to take that and declaratively state there isn't a single non-human on the whole planet is a little bit silly.
With the Asari culture that has been open to relationships with members of different races since the first game, even to the point where the species has developed derogative slangs against 'pure bloods', it's much more plausible to believe that there are other races on Thessia than there are aliens on Earth.
Heck, if you actually read the codex entries, Earth is hardly the center point of the Alliance. It was Arcturus Station that held the high ranked leaders and was the center of the Alliance military.... Which begs the question as to why Shepard was sent to Earth instead of the station where the Alliance leaders and parliament resided.
As I understand it, it's generally not down to governments to deal directly with disciplining military officers, it's down to the military and it's courts.
Plus, as we saw in the game, Vancouver wasn't necessarily *the* headquarters for the Alliance military, but one of several important facilities as there's also mention made of the UK based headquarters. The facility in Vancouver could just have been where Hackett sent the Normandy for refit and intentionally made sure Shepard was imprisoned nearby.
As for Arcturus Station; for starters, in ME3 you can actually go to the system for the first time in the series and even scan the wreckage left over after the reapers blew the station to pieces. You can even talk to Udina about the loss of the Alliance Parliament (including the Prime Minister) as a result of Arcturus's destruction. I'd hardly call that being swept under the carpet.
Sure, it may have made a little more sense if the prologue took place on Arcturus...but they started ME2 with you escaping from a burning ship and waking up in a space station. Starting ME3 with you escaping a burning space station might have been a little too similar.
Plus of course you needed to establish *some* connection with Earth, get a sense of the scale of the invasion, see the plight of the civilians (through the kid) and the comrades you leave behind (Anderson.) It also allows for the mission to Mars which is something I'd wanted to see since reading the codex entry in the first game.