Yeah, Thor would annihilate Superman because of that vulnerability to magic - unless, of course, the plotline and popularity required Superman to win, which it did in the Marvel-DC crossover from years back. Thor, however, did literally blow a hammer-shaped hole in the chest of Hyperion, Superman's Marvel equivalent. So, there's that.
Thor is also a better character, but that might be me being a liiiiiiiitle subjective.
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