I find that the less traumatic (for Me) option is to drown them, give them kisses before and after and tell them how sorry I am. Still a horrible option, but if they have no chance of being able to fend for themselves at some point, then it is cruelty to the chick as well.
Or keep it as a house pet with diapers, special feeding routine and lots of care. I am sure it is capable of love, but probably not capable of the good life of a chicken.
I had to make that decision recently and it broke my heart. But the chick would not be able to walk other than on its "ankles" as the toes would not leave the position that they were it the egg. Usually deformities in my chicks seem to occur with the last couple of eggs that take much more time to hatch than their siblings. I made the decision to end its life early rather than prolong its' agony.