[X] Stay with Mami and Madoka
One of the reasons I hate shipping is that it distorts the narrative to focus around one particular type of relationship, to the point of doing stuff that is objectively really kind of stupid if looked at in a light outside of "omg squee OTP."
Leave aside that it is fairly ambiguous about whether or not Madoka has any romantic attraction to Homura at all, and very much deliberately on the part of Gen Urobuchi who has no problem writing open homosexual relationships when he wants to. Leave aside that they both have serious mental issues that need to be addressed before they can pursue a health relationships. (Even though really it's like looking at Evangelion and deciding Shinji just needed to hook up with Asuka to solve all his problems.) Leave aside that they are fourteen years old, and probably just getting into romance at all, and how many first relationships weren't total trainwrecks, and that it's kind of creepy for Sabrina as the avatar of a hive-mind of grown men to be pushing them together.
No. We collectively are not the smoothest bunch of smooth operators around, to put it mildly. Persisting on trying to push Madoka and Homura together is at the very least going to wear on the patience and tightly-contained mental stability of Homura. She's been through hundreds of loops, all of which have ended in tragedy. Her distancing is a powerful form of mental self-protection, a shell against all of that pain. But for the time being it works. She is inhumanly focused and that shell can break in certain circumstances (like Kyubey telling her exactly why Kriemhild Gretchen is so powerful) but we can work with her on a very professional manner. She is utterly dependable as she is now. And of course there's no indication at all that Madoka needs to be hooked up to be happy given her web of valued friendships and her supportive family.
So bluntly there is no reason to pursue this further. Especially not now, when it risks poisoning a working relationship with our most important Meguca ally before Walpurgisnacht. If Homura and Madoka are meant to be together they can work things out themselves, probably after we actually have secured the future of the human race. That would frankly be a far healthier way for their relationship to develop, on their own terms, without a looming Apocalypse on the horizon. What right do we have to meddle in something between those two, that has no pressing threat to anything, and which may very well risk pissing off Homura to the point she becomes a lot harder to deal with?
All of this reasoning probably pointless if the QM wants the players to ship Homura/Madoka, granted.