This is somehting I think about a lot and we try to give some voice to in the Performance Menu. What is the intersection between Performance , Health and Longevity?
I think about it like a phase diagram:
All of these elements interact and movement along one line will, at the extremes, compromise other elements (for example the performance necessary to win the Tour is likely at odds with health and longevity).
Back to the original question: Is CF at odds with health and longevity? Depends on how you approach it. The WOD's as written will kill ANYONE if approached with 100% intensity every day. You have to find your own sweet spot and run with that.
Bill Fox has a great article along this line in this months PM as well.