According to the transcript of the episode in question, angels were not killed, they just left. Unfortunately I don't think it has been explained how and where they went.
Conversation between Dean and 2014 Dean about saying Yes to Michael:
Look around you, man. Half the planet's better than no planet, which
is what we have now. If I could do it over again, I'd say 'yes' in a
So why don't you?
I've tried! I've shouted 'yes' till I was blue in the face!
The angels aren't listening! They just—left—gave up! It's too late for
me, but for you—
Oh, no. There's got to be another way.
Dean talking to 2014 Castiel:
Yeah, I went mortal.
What do you mean? How?
I think it had something to do with the other angels leaving.
But when they bailed, my mojo just kind of— psshhew!—drained
away. And now, you know, I'm practically human. I mean, Dean, I'm all
but useless. Last year, broke my foot, laid up for two months.