As the Wikipedia mentions, it may be desirable to kill the animal without causing possibly prion-infected brain matter to be mixed into its bloodstream and carried to the meat before the animal's heart stops beating.
But the primary reason is unnecessary danger to slaughterhouse workers. I.e., where does the bullet go after it exits the cow's head?
Not that the cattle guns are completely safe, however. I remember when the drive-thru wave swept through the fast food industry. They were adding 'em on while the stores continued to operate. In one case a girl working the front counter got killed by a nail from a nail gun being used to construct the drive-thru pickup window.
One of the descriptions talked about using drugs to continue the putting down of a cattle. I assume this is not something to eat?