in a way, i can see why they went this route. If they did new stories, we'd be griping about everything having to be undone once the new movie hit. Similar to what happened to the old DC comics Star Trek series. They did tell new stories but then had to line the series back up with the latest movie coming out, which i remember people whining about.
This way, they can tell old stories but in a new way, without stepping on the toes of the next movie, especially with Orci there to help guide the book.
I loved it when the comics tried to "re-allign" themselves with the movie series. When I was reading through DC comics' first series (many years later) I not only loved the directions they were going in, but couldn't wait to see how they reconcilled themselves with the movie series. I was hoping for something similar here.
IIRC, those old comics said their post-STIII plotlines (Kirk on Excelsior, Spock on the Surak) were discussed with and okayed by by Harve Bennett.