I think it's a testament to the writers' abilities that they got us to care for their characters so much that we feel hurt for them. I suspect the way Act III unfolded was out of their control. The game was in development for a long while and the studio was pressed for time.
Now that Larian has breathing room, they're hard at work patching up the missing pieces. They're constantly recording new lines and adding features. They even added a missing cutscene for Karlach's Avernus ending on very short notice. So I'm positive they'll work something out for all companions.
