I believe you're incorrect in your interpretation.
The point of contention was always whether or not Peter's origin was magical in nature.
That's still up to the reader to decide.
That said, JMS did state that whether Peter's origin was magic or science, there were mystic forces that didn't care one way or the other, and sought him out. And yes, that includes the forces that resulted in his change in The Other. They don't care how he got those spider-powers, all they care about is that he's the spider-powered hero of this day and age.