Hey,
I have the same/similar problem. I've finished the quest, and I do not quite remember if I got any rewards for it (I think I did), but the quest is still active in my Journal, despite Pitli and her patients thanking me for the cure. I've ignored the problem so far, but I guess I lose out on some faction reputation? Anyway, hope you fellas at Obsidian can fix this, it's an otherwise stellar game!