I kinda a feel like Larian, or some at Larian, loves Shaowheart SO, SO, SOOO much that they just can't fathom people running the game without her, and are writing their story upon the assumption that she will be there, and going out of their way to force her into your party far more than any other companion.
IF that is the case, and they Want Shadowheart to be an integral central character to the story, then just go ahead and make her an 'essential' npc, make her a necessary part of the party, and be done with it - other games do this with characters that are of necessary importance the story, and it's fine, more or less, as long as you commit to it and write them well enough.
