In his post about the last episode of Puella Magi Madoka Magica, TWWK writes in one of his comments that Homura could work as a “John the Baptist” figure. I offer another interpretation: what about St. Peter? Homura was clearly written to be the ‘disciple’ who loved Madoka the most, despite her cold, anti-hero status in the final timeline. We see this especially in the flashback episode, how Homura was going to go to no ends to save Madoka, no matter what it would do to herself. Madoka’s remark, that she never knew she had such a great friend only adds to this parallel.
But Homura works as St. Peter in a couple other ways as well: firstly, her goal is to ‘save’ Madoka, when ultimately Madoka’s sacrifice is to save the world itself. There are differences of course: Madoka’s karmic power needs to accumulate through many timelines before such a cosmological reversal (hope triumphing over despair) could take place. Also, while Christ rebukes St. Peter for letting Satan speak through him, Madoka is the one who asks Homura to prevent her from becoming a Mahou Shoujou in the first place. Nevertheless, Homura is on a mission to prevent Madoka going to the cross, even though it is by the cross she will save the universe.
Secondly, the last scene of Homura walking in the desert reminds me very much of Pentecost in Acts. Madoka, being god of the universe at this point, is still able to communicate to Homura as she tells her to “do her best”, causing our apostle to smile and leap into the air, spreading wings which at first are reminiscent of a witch, but instead are filled with flowers, denoting that this is Madoka’s power of love that saved them all in the first place. Is this not, to some extent, like the Holy Spirit descending upon the Apostles, and thus the beginning of the Church?