Exp. breeders.... info needed

OK. This is a horrible question but it was irresponsible of me not to know before we started breeding. What do you do if a hatchling is deformed to the point of being unable to survive. How can you put them out of their misery w/out pain or cruelty???
Please don't think this is something I would do lightly! I STRONGLY believe physical deformity creates character and inspire strength...whether it be in humans or in animals!
We had a hatchling emerge today healthy, active and screaming like a banshee! ( I love when they get all worked up at being taken from the incubator!)
3 hours later her clutchmate joined us. She had a section of her shoulder/neck nearly fused to the side of her face! Her ability to eat or drink would have been difficult...more likely impossible! My heart is still aching for the little lady! I took her out of the incubator and held her for nearly 20 minutes...she died in my hands. She was very weak and small...so basically nature took care of it for me...But what if it hadn't!!
Man...I am such a SAP!!! I'm crying on my keyboard...she has shattered my heart!
I couldn't have stood to see her suffer or starve to death. There must be a way to deal with something like this??? Is there a way to put them down w/out being cruel or causing them pain?
I pray I am NEVER...NEVER...NEVER in that position again...but it was irresponsible to get into breeding w/out thinking of the possibility!
I still can't think of what went wrong...I've gone over and over it...the clutchmate is fine...a real beauty. The temps and Mom's diet...all was watched carefully! I just don't get it!
Anyone know how to deal with this???