I've been spying on this thread for awhile, trying to think of an answer, and I honestly can't think of any stories that shouldn't be told, for the reasons you and many others have touched on.
That all stories can be boiled down to different "foundation layers", but it's how you tweak the layers that matters. Even more controversial ones have nothing wrong with them on a foundational level.
Beauty and the Beast retellings can be abusive, and not only dismissive of the abuse but unaware it's there at all.
But they can also be really sweet, and be an age-old lesson about seeing through one's outer appearance, to the beauty inside, or about how ugliness can hide on the inside of the prettiest exteriors. Especially in Western cultures, this is a lesson we still have yet to learn as a whole.
All of these things are part of the layers that can be tweaked because the foundation itself is a neutral playground. I can't think of any stories that shouldn't be told. I can't even think of any tropes that shouldn't be told, because again, they're neutral until executed wonderfully, or poorly.
There are however elements to a story that I dare say shouldn't keep getting retold. Things I think help perpetuate the most harmful things about our cultures, our society, etc. But that gets really hard, because on one hand, shouldn't every be free to write exactly what they want? Or is it a situation that should be more along the lines of, "Yes, write what you want! But if it's harmful, please don't share it." I don't know. 
Summary
Edit: It's also important to note that even if the story at its roots are the same, a the first of a tale may not be what gets the message across to people.
For example, let's say we have Original Story. It's exposed to 6 people. It reaches Individual 6 but the rest didn't get it. Then there's Retelling 1, which doesn't get to Individual 1 and 3, but it does to Individual 2, 4, and 5. Then Retelling 2 gets Individual 3, and does nothing for Individual 1. Retelling 10, only a little different however, actually reaches Individual 1.
There are things I've see and read where I felt it was vapid, but someone else has a beautiful takeaway from it, some of which they may even feel is life-changing, while the things I felt were truly impactful flies over their head the way their preferred execution flew over mine. And that's why I see value in retellings.