I get that the Reapers are the baddest motherfuckers on the planet, but before as I've seen from cut-scenes as well as play, they're not perfect. If the Alliance could survive for weeks after the initial invasion assault, Capt. Bailey and friends could have organized a retreat. Look at who was on the Citadel before Shep went on his mission: Aria, Zaeed, Bailey, shit-tons of Krogan, Turians, Batarians and refugees from all over the Galaxy not to mention Alliance forces, Council forces, Mercs. I'm not saying they'd win against a full assault by the Reapers, but they should at least put up a decent fight.
We'll know eventually what happened. Hoping it'll be DLC or something where it'll allow you to play as Aria or Zaeed or someone interesting. Would be an interesting story as far as the mobster teaming up with the "Chief of Police" along with the world's most angry merc.