So, I haven't played the ending that you were talking about in the first post. In my game
I reluctantly allowed The Emperor to absorb Orpheus, and had him deal with the Elder Brain. Lae'zel hated me for it, but by the after party she had her new mission to take down Vlaakith, and told my character how much she respected her.
There's no obligation to have a fully happy ending, and I'd expect to have to make compromises. I haven't seen an ending that felt "unremittingly bleak" so I don't know how much my opinion relates to what you've seen. Maybe one for a future playthrough.
