Not necessarily. It depends on how the magic works. When CM hits him is he getting hit by magic or just a fist. Is magic just the fuel source or is it an area effect bending the natures laws. Say Superman was vulnerable to electricity and was hit by a robot powered by say electricity he's not getting hit by electricity but if he was hit by a bolt of electricity they would have a different effect. It's the same reasoning that Superman has been able to fight the magic beings in his rogues gallery.
In regards to the bold, I'd say both: Considering the nature of Captain Marvel, I would assume he is a being made of magic. Like Swamp Thing is made of vegetation, Cap is made of magic. So him punching Superman should be the equivalent of Superman punching a normal human being. To use your analogy: If Superman was vulnerable to electricity, this is like him getting punched by Zzzax. Still, I'm not familiar enough with Captain Marvel to say for certain, so I'll let it go.
I get your point even though I disagree some but what I was really trying to get across was is it's a matter of how you look at it. Your point of view is just as valid as mine because writers like to leave it questionable. They like to do that so they have room to do what they want with the story.