Do we know for sure issue 21 is set after the movie? That seems awfully quick. The Ongoing series didn't even begin until two years after Trek XI, and it was several months after that any IDW comic dealing with the movie was released, and that was just Nero's sidestory.
EDIT: Never mind. Just did some research and indeed it is set after the movie. Okay, but still that cover doesn't prove anything. I didn't expect for one minute that any of the main cast would leave, and the absence of Carol Marcus from that cover means nothing since we still don't know what her role in the movie is.