Yeah, fanon tends to warp our perceptions of the characters if we stick around it a lot, much like how Cupcakes has the power to alter our thoughts on a certain somepony. These recollections are especially prevalent when thinking of background ponies who we've built backstories and personalities for. I don't think of of anything other than muffins, mail, or Dinky when I see Derpy, or pants when I look at Lyra. Although, I don't have a problem with this, as I because all of us love good BG pony fanon.
As for the grimdark fic you mentioned, it never happened, you just have to remind yourself that it's aaaalll fanfiction.