I can see the temptation in holding back the super, but (for me) I would have a hard time holding back a deformed animal for breeding purposes. The possibility of passing along the deformity would probably nix the animal as a hold back for me.
I have not bred any snakes yet, but I have a good deal of experience breeding horses, mice and rats. No matter how pretty the animal, if there is an imperfection that is possibly/most likely the result of genetics (vs an injury), it does not go back into my breeding program.
Use your own judgement, but keep in mind that you can always produce more of the supers with future breedings, hopefully without the issues this one has.