This is how I've always seen how Shaft will end this series should they make the obvious and smart decision to continue Madoka...Madoka remembers her past timelines eventually, Homura gets super worried that Madoka will leave her, and Madoka makes the ultimate decision that we all know she will make: whatever the outcome, she will stick with her friends and stay with Homura.
There's many ways to go about doing that and Akiyuki and Urobuchi will of course make it absolutely stunning.