Well, the way I see it is thus:
Shepard has, to all intents and purposes, broken into the Reapers' freaking WOMB (ie the Collector base) and aborted their baby. That would piss anyone off. No wonder Harbinger PMS'd at Shepard until he legged it off the place. But yeah, I like the sound of the possibilities here. It's just that that last image in the game - seriously, go look at it again - with all the Reapers, thousands of them, approaching the galaxy. It gets stuck in your mind and you go "How the hell are we going to do this?" It took Shep one game to finish off ONE of the buggers, and that was the eager bloke who rushed right in and completely failed to listen to any of his mates. No doubt about it, it's gonna be a hard one.