[quote=@RBYDark]
Though Homura's involvement definitely means my third choice isn't plausible so I'll check for my second: how can Witches be treated?
[/quote]

Just for curiosity's sake, who [i]was[/i] your third choice? We could work something out if it's plausible [i]enough[/i].

Witches are fine, actually. In the new reality, Kyubey rules supreme in a dystopia version of the anime, so that little shit can do whatever it wants just to mess with the Magical Girls - including turning some of them into witches once again.