#scene zero

Another less important factor is that Mabayu DID say she didn't want to replace Madoka as the target of Homura's love, but having her still around in Wraith Arc probably would've done that. And Madokami does care about peoples ability to choose more than whether or not it is a good choice, hence her deliberate decision to allow Magical Girls to still make their wishes, just without the witch thing. Whether that is moral on her part is more of a larger philosophical discussion and beyond the scope of this post.

Also Mabayu's memory magic transcends timelines, so I'm not sure Madokami could've even undone it anyways. In fact Homura remembering wasn't even Madoka's doing. Even just going off the original anime, the idea that Madokami was responsible for that is only one possible interpretations and taking her dialogue literally it isn't the case. Wraith Arc, meanwhile, explicitly states that it was a miracle that was a result of their feelings for each other (or at least Homura's feelings for Madoka) and their connected magic. It was not an exception Madoka made for Homura, it was a phenomenon created by both of their desires.

I could also say that Homura did also want to remember Madoka, so it would also just be Madoka respecting her choices in wanting it to happen, but some might point out that Homura didn't want to forget Mabayu. However, Mabayu did want to be forgotten, at the very least so that she herself could forget, and with all the other things I've mentioned, then there wasn't much other option anyways.

And besides, if Homura remembered neither of them, she'd just go back to being moemura, and moemura wasn't very happy. She'd also never grow attached to the others in the same way she did Madoka, so while she'd have friends they wouldn't be close ones. Sayaka dies early on, Mami is a mentor who would be a bit too distant for her to fully become that close to, and she wouldn't be enough of a pragmatic cynic to get along as well with Kyoko as she could. Though their dynamic might play out a lot like KyoMado interactions tend to, depending on Kyoko's own emotional state. But also Madoka has a lot of very specific traits that seemed to cause Homura's bond with her. For instance her intense and frequent displays of (chaste) physical affection. At most the only other person to do that is Sayaka, but not as frequently or in the same ways, and she only did that WITH Madoka or other people she was extremely close to already. But again, none of this matters because Madoka wasn't responsible for Homura remembering anyways.

In fact, a lot of people who criticize Madoka while often acknowledging that the Law of Cycles is not in fact Magical Girl Valhalla (and if it was Rebellion would make no sense), fail to account for the fact that Madoka herself becomes very limited in her capabilities as the LoC. She is a Law. Not even a God, a LAW. It's actually crazy just how much agency she does have when taking that into account (and that agency is mostly spent on making her friends happy, as well as ensuring her own existence through Mabayu). Asking her to do more once she has acended would be like asking the same of gravity.

I will say, Scene Zero does read to me like the person who wrote it thinks that Madoka's ascension was an unambiguously good ending which again I think it wasn't. But it reflects just as poorly on Mabayu as it does on Madoka, since neither have been shown to have known that it would lead to what it did. And if Madoka did know about Rebellion, then she probably has a plan that will turn out okay in the end anyways. But seeing as she has been shown to not be all knowing, I doubt it. She just genuinely thought that Homura would be okay and not have to suffer anymore.

Both Mabayu and Madoka were at fault with that choice and I don't really blame them either.

This also isn't to say I wouldn't want Mabayu to show up again and still be able to get with Homura.

I just see them as equals regarding how well they treat Homura, and I don't think they would ever deliberately mistreat each other either. And I think Scene 0 itself is written pretty plainly as a story where while MabaHomu is likely, it must coexist alongside HomuMado in order to be what any of the parties involved actually want (even if Homura and Madoka are unable to be together for other reasons. Doomed Yuri and all that). Of course, canon isn't the be all end all of things, but what I'm getting at is that a large point of Mabayu's character is that she is not a replacement for Madoka.

That fact also serves as a nice counterpoint to the opposite argument, that Mabayu gets in the way of MadoHomu and is a Mary sue for doing so. Though it probably isn't enough of a counter argument to that, it is one (one of many, but that's beyond this post).