It's at the end a game about power and about the abuse of power messes up people's lives, that's a dark topic. I mean the two main songs that play throughout it all are literally "I want to live" and "The Power". All of the characters have certain shared aspects, almost of all of them were de-humanised (for the lack of a better term) by their surrounding and suffer the consequences. (Though it's probably least true for Wyll, who has a story arc that still somewhat mystifies me.) I don't think it is a conceptually bad ending to have the character that was exploited and deceived by her powerful employer to get nothing more than revenge and the option to go out on her own terms. It is a very real ending for someone in such circumstances. I just personally don't like it and am glad that she did get an end that fits the more hopeful tones of the story much better.
Also, I'd like to point out that if you have that cute character that the story really, really wants you to like, that character will most likely meet a horrible end. It's a trope. If a character death is supposed to have impact, you have to care for the character first. Beth March from Little Women comes to mind as another character of this flavour. It's not a new thing. Though I am surprised that they didn't imagine the outrage beforehand. ^^
