Last I knew anything about Magneto he was in the concentration camps for being Romani aka a gypsy, not for being Jewish. Which also made the Wanda + Kurt to give eventual birth to Nocturne angles a little more credible. Rom are naturally more inclined to stay within their own society because they are so easilly shunned and persecuted by others. Kurt is almost an ideal boyfriend or husband for Wanda in Magneto's mind. He Romani, he's an obvious mutant, he painfully chivalrous, and he's fiercly loyal. Granted, it's to Professor X, but still.
Once angle you could take here, although I'm reluectant to suggest it, is to make it the X-Men: Evolution Magneto that finds Harry. He was evil through most of the series but the visions of the future Professor X got from inside Apocalypse's mind show him teaching at the Xaview school for the gifted with the likes of Iceman, Wolfbane, and some of the other younger mutants laughing and carrying on with him in the Danger Room. Basically his apparent change of heart from fighting Apocalypse took root and he became the guy that was Xavier's best friend again.
Now picture Harry raised in that environment. Wanda and Agatha Harkness to guide his study of magic, a shit-ton of older brother, sisters, aunts, and uncles to give him some kind of happy childhood, and freaking Magneto teaching him how to not take crap from anyone.
Just as interesting as the comic versions, but with one extra advantage... there was never enough of Evolution to retcon, so Magneto is consistent. That alone makes it an attractive alternative IMHO.