My wife's family breaks apart the inside and cleans out what is in between the bones. My family just rinses the inside and then bakes it. Do you need to be super thorough when cleaning a chicken or is the baking process going to kill all the bacteria?
Assuming you're buying from a grocer or butcher (as opposed to gutting it yourself from scratch -- in which case, see below), as long as you cook it sufficiently, the heat will kill the bacteria in the cavities the same as it does the bacteria in the muscle. No special cleaning needed. In fact, I'd imagine that the germs on the surface in the cavity would get killed by the heat long before those near bone and covered by thick muscle.
If you are starting with the whole bird, check out http://butcherachicken.blogspot.com/. (Yes, it's exactly what it sounds like.)