I honestly wouldn’t be completely opposed to Magatha Grimtotem showing up again in the story, not to ‘take over’ for the Tauren or boot out Baine or anything, but to very much show her as trying to use the new Horde Political structure to her advantage.
Instead of her showing up as the head of the Grimtotem have somebody else do so in her stead, but it quickly be established that that person is very much a puppet of Magatha. Have her people be completely co-operative at first, offering the Horde what they need, manpower, resources, and soldiers, at a time when they are hurting for all three. The Grimtotem are one of the larger minor factions on Kalimdor, and them joining the Horde would shift the balance of power heavily in the Horde’s favor in zones like Dustwallow, Thousand Needles (isles), and Feralas.
However, in this hypothetical it is very much a tenuous thing, they provide what the Horde needs, and in exchange are getting the political backing of one of the World’s superpowers, etc. There’s a lot of ways to have this be done more so than just Magatha having some evil ‘kill everyone’ plot, and instead have her have more political goals that while not ‘good’ are not necessarily evil either. Something about getting the Tauren to a position of dominance, with Magatha very much wanting to consolidate political power into the Tauren races and make that political faction the guiding force in the Horde, with the Grimtotem slowly trying to ingratiate themselves with the other Tauren factions aside from the Bloodhoof Tauren.
Assuming Baine can be brought back to Azeroth, it could also be a chance to finally develop Baine in a way completely removed from the Alliance as he has to deal with internal Horde politics, and specifically Tauren politics in general. If Blizzard is so set on not having him just be a great fighter, than give him a political foe so he can develop his skills as a statesman, perhaps being able to defeat Magatha in the political arena in ways his father never could.
In this way, Baine could be developed as somebody who excels at Statesmanship and helps to steer the moral compass of the Council in a way that has him acting almost entirely within the Horde, and not with the Alliance.
Sadly… I have no faith Blizzard could pull off such a plotline, since there are no Kill X Creatures quests in it, and it would involve storytelling that Blizzard seems to have no interest in writing.