Skoll Shorties

a.) Saurfang goes to Outland in search of Thrall to save the Horde from Sylvanas. b.) Saurfang finds him, Thrall won't leave at first until he learns of what Sylvanas has done to Baine. c.) Thrall agrees to return but needs Doomhammer, and needs it powered.

d.) Thrall and Saurfang go to the Maelstrom and find that Magatha attacked it and stole it with her few followers. e.) Thrall and Saurfang confront her, kill her, and recover the Doomstone. Doomhammer is reempowered. f.) Thrall and Saurfang roll up on Orgrimmar and free Baine.

Magatha isn't really a character that needs to have the entire story written around her for a confrontation between her and another character. Baine's resolution with his father's death was the confrontation between him and Garrosh in the Shattering. She just has the macguffin.

You could also just flip the two parts of the quest chain and have Saurfang and Thrall break Baine out first if Baine has to be the one to kill her. Frankly in my mind Magatha isn't even killed by Saurfang or Thrall or Baine. She uses the Doomstone and ends up killing herself.

Magatha should get the death that was robbed from AU Gul'dan, where his own hubris was his downfall. In her desperation she uses it too much and it explodes (The potential to do so foreshadowed in both Cataclysm and Legion), killing her and the few Grimtotems left.