That is why Friendship is Magic is one of the very few TV Shows I let my daughters watch. Its fun, simple, and safe (its also interesting, unlike the other incarnations of MLP)
I think that is the Reason why the Show has taken off like it has (have you seen the ratings for the season two finale? Wow!) People want wholesome entertainment, and that means no Homosexuals, I.E. Shoehorning in a Gay Crew Member in Mass Effect 3.
Besides, Cupcakes wasn't so bad........
No, it's just a horror story. What's bad is that the canon Pinkie Pie from the show came to be almost universally identified with the Pinkie Pie in that story. Every video and pic of her was accompanied by comments about how dangerous and evil and psycho she was. There were even attempts to fit it in to the series itself, using the episode you reference as the time she started to lose her mind.
First, the idea that Pinkie has a separate personality named "Pinkamina Diane Pie" is purely fan convention. On the show itself she has no such split personality. "Pinkamina Diane Pie" is simply her full name (the only time she is addressed by that name on the series she already has her "happy" poofy maned look). She gets grayer and her mane and tail flatten when she's depressed. But there is no split personality. And in the episode in question she was merely sad and angry about being "betrayed" by her friends. She wasn't even contemplating doing anypony any harm. Come on, people!
For another thing, the Pinkie in "Cupcakes" isn't depressed Pinkie at all, but happy poofy haired Pinkie. That's what makes it such a horrific fic.
Personally, I blame the "evil clown" thing. Pinkie's just too happy to accept on her own terms, so she must be some sort of terrible monster. It's this that I object to, and it's this protectiveness that has made her my own personal favorite among the Mane 6 (even though I'm nothing like her myself).
Someone with artistic talent needs to draw a pic of "Pinkiewise the Dancing Clown" with the "dead lights" in her eyes as she opens her mouth to show all those horrific pointy teeth.