It's not so much a moratorium on running the ball, it's the coaches discouraging Newton's persistent attempts to commit suicide by linebacker to get an extra yard when you're up 7 in week 9.
You're right though, when Newton was willing to charge into the arms of defensive tackles, he'd have entire defenses key in on him. It was like having a guy who, just by being on the field, was taking half the defense out of the playcall. That's part of how they went 15-1 with a terrible receiver corp. Now it's a QB spy + 1-2 other guys. Newton can't throw on the run for crap (see his second pick yesterday), so once he is running he's not much of a threat there.
As for the game yesterday, Chicago has a great defense, their offense is awful, from the coaches to the personnel on the field. I don't know if Benjamin is lazy or if the blown ACL took away his explosiveness, but he let that corner box him out easily on the pick 6. And he had half a foot and 50 pounds on the guy!