I think pithing (destroying the brain) is the quickest and pain free for the animal. It is very hands on and I don't think some keepers would be able to do it. I refuse to put any animal in the freezer.
I also keep a hungry king snake on hand to dispose of any bodies. Hasn't happened yet and I hope to never have to. But I would feel a little better feeding the cull to something rather than going in the trash.