I remember reading comments from Bob Orci on another site that he was disappointed they were pulled. Since he was part of the Abrams team, if Bad Robot had blocked them somehow he wouldn't have been disappointed.
He wasn't the one in charge, though. Just because they were all working together, that doesn't mean they couldn't have disagreements. For instance, we know that on STID, Orci and Damon Lindelof argued over whether to make the villain Khan, and Orci lost. So he didn't always get his way.