I think they changed the story well before deciding to make him a companion. I suspect that if we want to figure out what happened, we need to focus on Isobel, Shadowheart and Aylin, rather than Halsin. I think Halsin was just a casualty of a change in direction surrounding those characters, rather than being the focus.
If you really look at Shadowheart's place in the story and how it goes in act 2, there's actually a lot of stuff that doesn't really make sense. Shadowheart is apparently meant to become Shar's chosen by using a super important spear to kill Aylin. But why is killing Aylin that important? So important that it warrants a prophecy. Also Kethric apparently had to send Balthazar to seek out Aylin despite those two being the ones to capture her in the first place. Also, why does Shadowheart's hair turn white if she abandon's Shar? that just never comes up even though it's not like it used to be white and her hair went black after she was kidnapped. And why does Aylin instantly have insight into this random girl who came before her? Also, Halsin would have known about Aylin, since a divine emmissary visiting a nearby village on the regular would be THE thing everyone talks about and now way would he not have heard about it.
I think that there used to be a story where Shadowheart and Isobel and Aylin were way more intertwined, and that changed in a big way.
Shadowhearts hair dies come up: She says, she died it to mark that big change in her life.
