Captain Marvel hit Superman with numerous magical lightning bolts and Superman was still standing... then they got an atomic bomb dropped on them and Superman lived... Captain Marvel did not.
Thor would not know automatically Superman was hurt by magic. Superman would know automatically that Mjolnir was the source of most of Thor's powers... He could take advantage of that before Thor could take advantage of Superman's weakness.
There is no way they are nearly as strong... An Island? Or WarWorld?