Usually with such severe birth defects the baby animal would not live long or have a good quality of life while it lived.
I think this is the hardest part of being a breeder is coping with the babies that just can't make it.
A newborn kitten may not have all its pain receptors connected (just like eyes and ears are not open) chances are when the nerves knit in a day or so the kitten would have been in serious discomfort.
I think you did exactly right even though I agree its a very difficult decision to make.
I would have found it less humane if the kitten was allowed to linger and suffer.
Hope this helps you!
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