I asked Bob Orci via Twitter and he responded:
@cseremisi: is IDW's Star Trek Ongoing canon from Star Trek Into Darkness point of view? ” New interview will answer that.
So it seems that there is a new interview coming about Star Trek Ongoing. This is important because in issue #1 and #2 there was Gary Mitchell. So I really begin to think that we might get Mitchell after all, I don't see another issue of the comics that would conflict with the movie.