I remember reading about a disease called Kuru or laughing sickness in the 70s. It was listed in the Guinness book of records as the worlds rarest disease. The only people affected by this were certain tribes in Papau New Guinea that practiced ritual cannibalism by consuming those in the tribe who had died, the brain and bones were part of this feast.
To add protein and other nutrients to the diet of livestock, it became common place to make a supplemental meal from the unused portions of cattle which included brain and spinal tissue to animal feed. It is suggested that this might be the original source of mad cow disease. Such practices have been halted as it was proven that mad cow disease could be transmitted to humans.
There is no conclusive evidence that CWD can be transmitted to humans through the consumption of deer meat, with that being said it would probably be a wise move to not consume brain or bones of processed deer. Deboning makes good sense.