It's true that Murray didn't "run to daylight" with the best of them. BUT, his special skill was being able to bring people in close, then use a combination of quickness and power to eek out a few more yards.
I think the two are connected. He knew he was special at making people miss in close quarters, so he often ran TOWARDS people in order to use his best asset. So, while he "left" yards on the field, that same special move also meant that he gained a lot of yards other backs wouldn't.
Since it was the single season record for the 'Boys, I'm gonna say he gained more than he lost.
Still, that also means that a back with a different skill set (running to the holes) could gain almost as much.