You probably already know this, but it plays on an old saying "Don't throw the baby out with the bathwater". The saying supposedly comes from the practice of the whole family using the same bath water for a given cleaning, with the baby being the last. The bath water would be quite dirty you see and one wouldn’t want to mistakenly discard the baby with the dirty water. Thus a metaphor for not throwing out a good idea along with a bad application of that idea.
Now more to the root of your question, how does that apply to the story itself? I'm not sure. Maybe the act of taking the child super away from its family of normals came with a lot of filthy, negative baggage?
Actually, I don't recall hearing that expression. Thanks for the answer! I like to use outdated colloquial expressions and watch the ensuing reactions (usually eye-rolls from my wife until I use it enough that she starts picking it up). This one's going on that list!
Even if the application to the story isn't immediately clear, at least I understand the root expression now.