I agree that we don't need Kryptonians being any more susceptible to Scarlet Witch's powers than anyone else. The change in Man Of Steel to allow for special attacks to have a better chance against Superman was entirely based on his "weakness" to magic. So the extra vulnerability to magic is built into Man Of Steel. This also made him vulnerable to other types of special attacks, but at the time it was the only way we could figure out a way to include his magic weakness.
Otherwise, though I'm not overly familiar with her, I like the direction she's headed.