I strongly reject the interpretation that Homura could have died from that fall, or that it signifies her reaching a point of ultimate despair. She achieved what she wanted at that point (even if it's obviously bitter sweet for her), and is all powerful, so it doesn't make sense from either perspective (to me, at least.)
I think it's more a case of "be care what you wish for": Homura has Madoka, but at the extreme cost of literally sealing her away and effectively denying her her own free will. She gained ultimate power as an act of extreme selfishness: Homura didn't want Madoka to be happy the way she chose, Homura wanted Madoka to be happy the way she chose.
And Madoka and the fandom wanted Homaru to be happy the way they chose.
If there is to be happiness through tyranny, it seems Homaru is the one most deserving to be the tyrant since her tyranny is the only one that solves the basic problem by making the guys who caused the problems suffer the burden of containing them.
The incubators created a world where all magical girls suffer.
Madoka created a world where only she and Homaru suffer.
Homaru is the only one who created a world where everyone with good intentions can be happy.
Both of the previous 'Gods' proved flawed Gods.
Obviously, the story won't stop here. Homaru felt that she needed to be the bad girl in order to forcefully create the world that any of them would want to live in if they thought about things in a sane manner.
As always with these online drama's it seems that not the story the fandom rejects is at fault, but the fandom that rejects the story simply because a dark-haired character is not portrayed as a helpless girl that needs saving.
The only reason there is so much whining about Rebellion is because Homaru was portrayed as empowered,
She took what she wanted and did what she wanted and the girl with the lighter hair color wasn't portrayed as a flawless omnipotent being. (Ironically, because in this case, the girl with the lighter hair color was a God)
Judging from so many of the doujinshi and comments here, what the fandom wants is a shy, helpless Homaru that needs to be saved and an empowered, dominatrix Madoka.
In other words, the fandom wants two characters that have nothing to do with the official portrayal of the characters.
In other words, Homaru being the one to suffer most from the beginning because she was created by the writer to be a cliché melancholy, sickly girl that became so obsessed with Madoka that if there was a lesbian version of the Bechdel test (and there needs to be one very urgently) this franchise would fail it so hard it would make your ears ring isn't enough for the fandom. They want Homaru to be a sleeping beauty who always waits for her Madoka to save her instead of a confident girl who is able to save Madoka from herself.
Yes, Madoka was going to take her to heaven so they could be together forever, but still, she would only exist for Homaru. And she would still suffer from having to take the burden of relieving everyone elses suffering on herself.
But from the fandom's pov the light haired girl was empowered and saved the dark haired girl, and that is all that matters to them.
In Homaru's universe, she and Madoka can spend time together and be happy, while the bad guys take the burden and both of them exist for everyone else in the world.
But: "Oh no! the dark haired girl is empowered and saves the light haired girl! We can't have that! This story is trash! Let's ridicule it as much as we can!" As if you couldn't have ridiculed the story the fandom wanted much more easily ;)
If there is a sequel I hope it will be as far from being what the fandom wants as can be.
I hope rather than there being a confrontation, Madoka's existence will be threatened because Homaru separated her human form from her divine form. I hope that will force Homaru to save herself from the obsessive nature of her love and recognize that since they are both deities now (The fandom's insistence that Homaru couldn't possibly be as powerfull as a fully powered Madoka is more proof of its perverse obsessive desire for Homaru to be helpless and melancholy) they might have a way of solving the problems they have faced from the beginning if they tried to understand each other better and work to find a way to solve them that would not envolve either of them to tyrannically decide what the best solution is for everyone.