Whilst I understand your views, it's important to remember that the budget is incredibly tight for this project. If CBS went back to re-scan the whole episode (which may be the case if their original scanning was cropped for non-FX scenes), the time and expense would be HUGE. What's more, it would divert funds and man-hours away from other episodes which wouldn't benefit as much as they would have done otherwise.
In perspective, "Sins" is still perfectly watchable, and as someone pointed out - it was only really noticed through looking at the credits text.
OK, let's hope it is part of their learning curve to first compose the episodes with full aperture and then leaving the cropping for after they ended -- and properly saved -- a full aperture version. If that was done in the first place, it would be piece of cake to create multiple cropped versions, without spending so many man-hours.
Interviewer, since you're talking so much with them, do you know if they are making 16x9 versions (cropped, as the docs suggest) for syndication purposes?