Holy shit. This explains so much. Seriously. And it actually ties into Halo:CE for me.
There was a part in Halo where after you land in the escape pod, you are supposed to protect these marines at a fort or whatever it is. As I approached, Private Bisenti greeted me: "Thank God you're here, Master Chief... I thought we were in real trouble."
That's when I stuck him with a sticky grenade.
What I did then was go up to every marine and either shoot them, melee them in the back, or whatever it took.
Afterwards, Cortana says something that I found chilling: "We couldn't save them..."
I thought this was Cortana trying to get our story straight for when we had to report to our superiors. But no, it was something far deeper than that. She was trying to smooth things over between my id and ego. It wasn't something to tell everyone else about why they all died. It was something for the Chief to believe.
Didn't I kill all those people? No. We couldn't save them. She puts "we" in there because, I believe now, she needed to take some of the blame from John in order to keep things working. And also because in that moment, she failed in her role of keeping John's true hatred of humanity at bay.