Shoot, I thought they were canon too. I thought that was the point of the new comics being done by JJ's people.
The point was to keep them as consistent with canon as they could, which isn't the same thing as actually being part of the canon. But I think Bad Robot underestimated how difficult it would be to keep the tie-ins consistent with an ongoing canon. There's a reason the only really canonical novels and tie-ins (like the Del Rey Babylon 5
novels or the Buffy
"Season 8/9" comics) are those that come along after the screen series has ended. Ultimately, tie-ins are always secondary to the core work and must yield to it, unless the core work ends.