The fact that the IDW comics are being considered canon was confirmed directly by Roberto Orci. He is one of the writers and producers of this movie and also had a similar role on the first one.
Besides this, you must of course realize that this is all part of a large marketing and media effort based on the Star Trek property. There is a level of organization here and when the decision was made to start an ongoing comic series it was done so to appeal to certain fan's desires to flesh out and expand the rebooted universe. To not have a level of continuity between the various media being used to tell these stories would be illogical.