Cassandra Nova isn't just a clone of Xavier. And they are not equals, nor is she just "slightly above him".
She is Xavier at his fullest potential, as she has access to his entire genome, including all his latent traits and powers, which is why her telepathy is much much more potent than his, and why she also has a bunch of powers like telekinesis, phasing, etc. on top of her mummundrai powers - astral form, DNA copying, and creating a body from a mess of biological tissue.
As for this battle with Superman, Supes could 10 count her I suppose with an immediate speed blitz before she reacts (assuming she doesn't have auto-TK shields). But then she'd just be left with an astral form... which I suppose could still mind rape him.