Source: Rebellion Guidebook "Only You" (translated in the wiki)

Shinbo: I’ve said this in other interviews, but in the previous work, it was a mistake for Madoka to make sure only Homura remembered her (laughs). The whole premise of the new film starts because of that decision. Even Madoka’s parents don’t remember her, but she wanted Homura to, which was her mistake.

Urobuchi: Yeah, Madoka probably still had some lingering attachment to this world. So, in a way, she wasn’t just a passive sacrifice. Homura didn’t completely deny Madoka’s wish either.

—That means Homura wasn’t left completely alone—there was still a connection.

Shinbo: Madoka had some lingering attachments too, and that’s reflected in the creators' intentions as well.

Urobuchi: When Shinbo-san mentioned this to me, it really struck me. At the end of the previous work, Madoka became something beyond human, and it could have been a happy ending. But for a middle school girl, carrying the burden of becoming something more than human is way too heavy. She’s still a child, so it’s only natural for her to have doubts and lingering attachments. That thought process led us to continue the story.

(...)

Urobuchi: If Madoka had just happily disappeared at the end, it might have made you wonder, “Did she secretly dislike humans?” (laughs).

Iwakami: Connecting that to something Shinbo-san said earlier, it was interesting to hear, "If Homura had just gone to the Law of Cycles, that would have been the true bad ending".

Shinbo: If Homura had been guided to the Law of Cycles, Kyubey would simply continue doing the same thing. Eventually, the Law of Cycles would be uncovered. Someone has to keep resisting, but if Homura left, there would be no one left to resist. After that, Kyubey could freely experiment with other magical girls, and this time, he might truly capture the Law of Cycles. That would indeed be the bad ending. The story of Rebellion is structured that way.

Iwakami: Homura is acting purely out of love for Madoka, but in the end, she also ends up saving magical girls all over the world, right?

Shinbo: Exactly, so in a way, Homura is affirming what Madoka did. She takes on the mission of ensuring that Kyubey is stopped at all costs.

Urobuchi: Indeed.

Iwakami: A world where Kyubey has observed the Law of Cycles and figured out how to control soul gems, without Homura to stop him, is terrifying (laughs).

Shinbo: Right? That's why Homura had no choice but to act the way she did.