Many of your complaints (about the rest of MSY "destroying Homura's life's work") seem predicated on Madoka's godhood not being a instant win condition for everybody.
Just pointing out that Madoka had literally
no reason to believe herself entirely exempt from the system, no matter the wish, just that she
could make any wish. The end-result could have
easily gone awry and caused Madoka to become an evil goddess, since the system
heavily leans on the concept of equivalent exchange. It could have even broken her as a person altogether with the wish or time, making her the biblical god with all that entails, or is gradually corrupted by her own hubris and omnipotence even ignoring her 'friends' agency and feelings entirely. Absolute power corrupts absolutely, after all, Homura has shown to do jack shit but torture herself with unlimited power, but Madoka 'I want to save everyone' sitting on her laurels with infinite power? Doubtful.
There
is precedent with wraiths replacing witches, as well. Point being, she had a good 50/50 chance of basically destroying the universe or becoming the big evil, while basically destroying the sole person who made them powerful enough to do so in the process at the moment of their victory. Just because it
didn't end catastrophically doesn't make it
okay. Worse, it was calculated, planned, and not loop-exclusive, this is something Madoka had been concealing for dozens of loops, at least, and executed in an exceptionally brutal method.
The epilogue was a slap in the face too really, Madoka seems borderline abusive, and more importantly, barely seems to care or empathize with Homura as a person beyond anyone else, like she's just another of her friends. I think the worst aspect is that they victim-blame as hard as possible, and immediately asks for a wish when she's at rock bottom, rather than actually helping her. I saw Homura's affirmation more as her giving up any delusions or hopes of anything she had entirely.
PMMM is all about equivalent exchange, though
who pays is an entirely different question, and even then, like soul gems, with every blessing, an
equal, often ironic curse in fate. Sayaka paid for Kyousuke's hand to be healed, but lost her reasons to do so, his heart and her heroism. Kyouko paid for her father's words to be heeded so they could eke out a living, but he saw her as a witch and went mad, killing everyone and subsequently rendered her homeless and destitute. Mami paid for her own survival, but unintentionally led many innocents to their deaths and lost the connections that made that worthwhile.
However, Madoka and Homura are a bit different due to their acausal, atemporal natures. From an achronological perspective, Homura paid to save/protect Madoka through a decade or so of constant failure, hatred from her old friends, and immense suffering. Due to the nature of her wish, Homura becoming Homuicifer was a fait accompli the
moment Madoka made her wish, because the scales must always be balanced, and if an godlike entity comes into existence representing hope and offers salvation to puella magi as they die, one
must also exist representing despair. If Madoka gained karmic potential from Homura's efforts, so did she herself, for woven and weaver are equally important. For both of them, their beginning's and ends are intertwined so heavily that neither can likely exist as they are without the other either. Superceding the system for good needs them both to work together, as both their respective worlds are flawed in their own ways.
Even Godoka herself isn't
wholly exempt from the system, it just
seemed like it due to the nature of her wish by destroying Gretchen's endpoint and basically committing temporal suicide. Just like witches were replaced with wraiths, Gretchen's absence necessitated being replaced by Homucifer. Canon Madoka didn't actually change the base mechanics
at all, merely redistributed it with grief cube availability, comparatively weaker wraiths, and Incubator incentives shifted to want to draw out a puella magi's lifespan to maximize ROI, from them leading the sheep to the slaughter to mass-produce witches, to puella magi becoming what are essentially farmers.