I understand where you're coming from, Chemy
. While I wouldn't use the term "rape", I do agree that Fluttershy's mind was violated by Discord (it shocked me a bit when it happened, too). Everyone will have a strong opinion about this episode, I believe, since it involves what may arguably be the best villain of the series so far.
I'm still certain we haven't seen the last of Discord's chaos, and if it did end up being used in a way similar to "Q" (the unknowable entity who is chaotic), then I think that would be satisfying for myself. As I said, I enjoyed the episode, but each person is different. I am still no fan of "Lesson Zero", even though it's very popular in the Brony fandom. I just don't like seeing my ponies go crazy, especially
the one I consider best pony, and though I have watched "The Return of Harmony", and I like Discord as a villain (and love John DeLancie), I don't watch it much because I don't like seeing what happens to the ponies in that story. That's why it doesn't bother me when people love an episode I don't like, and dislike an episode I love. So, I do get what you're saying here.
Though if I did have a particular nitpick, it would be the "gravy" scene. Gravy is a meat based substance. Our ponies are vegetarians. Though there is vegetarian gravy, so I guess it could have been that. Still, the gravy in the crotch scene seemed out of place.