A mildly interesting discussion in the comments on the NYT Freakonomics blog.
I like the statistical point that it makes more sense to compare trip to trip and not mile to mile, since people who bike likely have shorter commutes. I also like the point that it would save more lives if people wore helmets on ladders instead of helmets on bikes.
Will biking kill you? The short answer is maybe. But if you live, you'll probably be very healthy and live longer.