I remember the scene from the novelization as well. It stuck out because of how "wrong" it felt. The oomic story had Superman simply get a momentary upperhand on Captain Marvel and keep Cap from dodging the lightning, Maggin made Superman immune to magic.
If I could find where I packed up the novel I could give you a full quote or at least a page reference. Alas i only have my memory, but it's pretty clear on this one. Maggin made Superman able to resist magic once Superman "understood" the way magic worked.
If you could transcribe the passage when you have a chance, I'd much appreciate it.
By my stars, I'd swear nothing of the sort is in the KC novel because I did read the durn thing and I feel as if I'd remember something like that.