[Rampant _PMMM_ spoilers everywhere]
It's been a while since I watched Madoka Magica, but I think there's definitely something interesting going on with its story. What makes it kind of odd, I think, is that Homura is probably the Protagonist, whose Goal is defeating Walpurgisnacht without Madoka becoming a magical girl. Trouble is, this is pretty well obscured from the viewer for most of the season; what we get instead is Madoka and Sayaka digging into the magical girl community, and Madoka deferring on her choice of wish. So perhaps Madoka is the Protagonist, with a Goal of "choose a good wish that will save the world?" I think that makes Homura sort of a complex Contagonist, always needling and probing in just the right way to delay Madoka's wish and so prevent the previous time loops that ended in heartbreak.
So you're definitely right that the relationship between Madoka and Homura is key to the main front. (Kyubey is... Temptation, I think. Not a full Contagonist, since Homura is Hinder, but Temptation and maybe Logic, too.) As to Sayaka... I'm a little leery to start throwing around a second storyform, in part because I prefer thinking of subplots as facets of the main plot rather than a second plate to spin, but also in part because I don't know if I ever really empathize with Sayaka. I pity her and her lot in the story, but I never think, "Wow, I know what it's like to be the knight trying to be the sin-eater for the entire world." To me, Sayaka's arc is a cautionary tale as part of Madoka's arc--"Don't let your wish consume you, like Sayaka's did." I do feel like I'm Madoka throughout the show, seeing all the other magical girls and wanting to do right for them. (Help, I'd imagine, to counter Homura's Hinder? Which of the two is the Change character? Madoka, for finally making the wish that saves all magical girls from slavery, or Homura, for finally letting Madoka go?)
(...Was Kyouko the red magical girl, or was Kyouko the boy Sayaka liked that rejected her? Like I said, it's been a while. The -ko suggests it's the red-haired girl, but... now the cracks are showing in my memory. I don't remember her role in the story that well. I remember the beginning, the bit with the eggs, the part where Sayaka falls, and then the ending with Homura's reveal and Madoka's wish. I haven't seen the movie.)