I noticed that if you go in the chapel to loot and kill all the other looters, there's a point in which Shadowheart just plain disappears from your camp without explanations.
I heard companions can leave your camp if they don't like you, but I checked and she was neutral with me. I'm also assuming that should she leave the camp because she doen't like me/my actions, there'd be at least some kind of dialogue in which she tells me she's leaving. This happens only after the big fight with the looters, when you use a lever to access the rest of the chapel/crypt. And yes, I did try to access the crypt from the hatch, and as soon as I entered the place, Shadowheart disappeared from camp.