Spoiler! :
Interesting idea. That is the first time I have read that one, but that does not make it wrong per se. In any case, we know that Homura is from an alternate future with implication that she and Madoka were close friends. By Homura's tears, I can guess that Madoka might be dead or missing in Homura's reality. Alternatively, Homura became a Puella Magi to correct the errors of the past to prevent Madoka from dying or something to that extent. If anything, it seems that her presence is not helping the situation; in fact, it seems to be slightly aggravating it, especially with respect to Sayaka. It would not surprise me if the witch at the beginning is Sayaka. It also would not surprise me if Kyuubey turned out to be a witch or the "boss" of the witches in disguise. The whole approach that this series is taking reminds me of Claymore gone Shugo Chara in the worst way possible, which ironically makes the series that much more interesting.
