Exercise does cause damage to your body, both structural and oxidative. Fortunately, that damage triggers repair mechanisms which make you stronger than before. See http://en.wikipedia.org/wiki/Hormesis#Physical_exercise
An aside: Reading this article made me wonder why I tasted blood after particularly hard workouts. Apparently the heart can pump with enough pressure to rupture some of the capillaries in your lungs. A tiny amount of blood leaks out and gets aerosolized. At least, so says this paper: http://abughrai.be/Vulnerability%20of%20pulmonary%20capillar...
Seriously, how can one not already realize this? You can of course work yourself to death, but you'd think people would have noticed how much healthier they feel when they have been exercising, and how quickly they deteriorate when they haven't.
The above poster is - as I understand it - pointing out that this study does not necessarily contradict the hypothesis you mentioned. A small amount of exercise is shown to be beneficial, but it is entirely possible that larger amounts of exercise are detrimental.
Do you know if any research has been done into that hypothesis? Because - failing a confirming study - it does not seem to fit with anything I've heard. I mean, maybe some organs can get overwhelmed if metabolism is pushed too high too quickly, but in general I doubt that a fast metabolism even correlates with lower life expectancy.
I remember reading somewhere the opposite hypothesis. The argument went like this:
more exercise --> faster metabolism --> faster consumption of your body utilities --> lower life expectancy