So, There are two associated quests to kill Karlach. The overarching "Hunt the Devil" quest, and the specific "Kill the Devil" quest. I got the quest to kill Anders from her, went and spoke to Anders, and decided to go back and kill Karlach instead.
Doing this only completed one of the two associated quests, the 'Hunt the Devil' quest completed, while the 'Kill the Devil' quest did not, and is now permanently unable to be completed.
EDIT: After posting the pic, I realize that - for whatever reason - it also marked the "Kill Anders" quest as complete, even though the image shows that i turned Karlach's head into him, and did not actually kill him.