I might be wrong but personally I think it really depends on your cat.
A cat's prey drive will always exist and depending on your cat it will also try to hunt down your snake if it moves. Cats hunt moving things. If it doesn't move than it's not interesting. That being said, I don't think the smell associated with playing will make your cat hunt the snake. Your cat will hunt the snake if it moves, that's what cat are like. You know your cat best, so I believe your the best one to judge whether it would be okay for this cat to play with the skin or not. If you believe your cat would attack your snake, then don't use the skin.
My cat for example is scared of almost everything and she is really scared of my snake (she has watched him through the glass of his enclosure). No way in hell would she go near him (and I wouldn't let her anyway) or his skin for that matter. If you know your cat is quite bold, then don't try to encourage this behaviour. There are many ways to keep your cat occupied without using the skin. That's actually my main point. Is there any reason to use the skin other than that your cat was interested in it? Can't it just have another toy?
I don't believe the snake skin will make a snake murdering kitten out of one that would not have tried it in the first place. But honestly it is just not necessary to use the skin as a toy, is it?