Check out my monthly column at Endurance Corner, where I discuss the potential for (too much) exercise over the long term to cause harm to the heart.
All things considered, this issue hasn't been studied very well. I review some of the pertinent scientific studies that raise important questions in this regard. The findings are certainly preliminary and beg for more research.
In my mind, the health benefits of exercise are well understood, though. I wouldn't stop exercising just yet!