You know, I can't help but wonder if we could solve the biggest problem by having Madoka make a slightly better-worded wish. So that she doesn't personally remove every Witch from existence, thus becoming a Concept, nor would she metaphorically take in all of the grief onto herself as a result (or whatever).
I mean, if Madoka's potential is basically "yes", why not take advantage of that? Just make sure that Madoka's own well-being is covered by the wish (or at least, not specifically sacrificed).
Of course, Moid won't let us have survivors, so shit is fucked no matter what.
Or Cherno Alpha shows up to save the day by punching Walpurgisnacht in the face repeatedly ("CHOO CHOO MOTHERFUCKER").