Yeah, it never feels great to tell someone simply not to apply.
But in fact the very experienced college counselors at our feederish HS will apparently do just that sometimes. And reportedly MIT is one of the top colleges for that happening. Meaning apparently they have a good idea who might get accepted to MIT from our HS, and if a kid clearly is not in that group, they will encourage them not to apply.
That said, I’m not in a position to know that is the right advice for the OP. I just do think it is sometimes the right advice for some kids.