Dude, that's a legitimate weakness for Superman. And when you figure that Thor and Superman are evenly matched in almost every other area, the only advantage one combatant may get, is the weakness of his opponent.
I don't think Superman is incapable of beating Thor because of his weakness to magic. I just believe that the weakness, combined with Thor having been a warrior for Lord knows how many centuries (or eons for that matter) make for enough of an advantage that he can beat Superman. While I referenced Kingdom Come as a prime example of how mystical lightning can damage Superman, you can also reference JLA/Avengers #2, where Superman beat Thor in a physical slugfest.
I'd be willing to bet that physically, Superman is stronger than Thor, and is a good enough fighter that a straight up punch-fest could go in Superman's favor. I don't know that Thor has ever decisively beaten the Hulk or Hercules for that matter, and Superman is easily in both of their leagues. I just think that given the advantages that Thor has magically and tactically, he can beat Superman.
Superman could indeed win this battle. Here's the scenario:
With his obvious honesty and natural nobility (Let's face it, there's no denying by even Superman's biggest critics that he's the most "pure of heart" all Superheroes with only Captain America probably coming close) , not to mention the lives of Earth hanging in the balance, Superman would be perfectly capable of lifting Thor's hammer, much like Beta Ray Bill did in Thor #337 (yeah, I know my shit ).
Much like in JLA/Avengers #2, Thor attempts to strike Superman with Mjolnir, but Superman catches the hammer in mid-strike. But unlike JLA/Avengers, Superman manages to wrest the hammer from a completely surprised Thor (who rarely meets someone who is not only in his strength level, but who can also lift his hammer).
With Thor's weapon in hand, Superman doesn't just have a hammer, he also now has all of Thor's powers, as the enchantment on Mjolnir isn't just that if you're worthy, you can lift the hammer. It's that you'd have the power of Thor. That would include Thor's power over the weather, thus negating Superman's weakness to the lightning strikes (which Thor could no longer summon due to Superman now possessing the Hammer. Without that weakness, and with Thor's hammer in hand, it becomes Superman with the advantage. A battle that could have gone either way with the slight advantage to Thor due to Superman's weakness to magic becomes a clear advantage for Superman who no longer has that weakness, and also has Thor's hammer. Before too long, he last man standing is the last son of Krypton.
-Corey