Less complicated, take a wide bladed knife and jam it straight down into the mid line of the head, closer to the neck. Check out the diagram someone already posted, the brain pain is not exactly between the eyes. It's closer to the neck but if you are using a large enough tool, a hatchling that is weak and deformed ought to be able to be very quickly culled. It would be best to be calm and in control because if you slip,you could hurt yourself as well. :/ I know it sucks to have to think about but you are doing the best thing if an animal is truly that messed up. I've seen too many examples of heads lasting longer than one would expect. It's why the guillotine went out of fashion, and considering that snakes have a slow metabolism, it may take them much longer to go out with that kind of method.
I would personally recommend that if one has a vet close by to get it euthenized properly. It was hard to put down my gal with a tumor, but the vet did housecalls. A few places will do emergency euthenasia and I would call around and see what you can do. I'm lucky enough to have a really awesome Dr.