Let's assume, for a moment, that the author has never heard of these laws. What then is the motivation? I have found a few, some serious, some not as much. What the heck, I'm supposed to be sleeping, but I'll take some time to explore why people write gory or disturbing MLP fanfiction.
First, and probably formost, is contrast. The land of Equestria is a bright, happy land, where multi-colored ponies can sing and dance with relative peace. Sure, you may run into some jerks, some hazards, and even a few monsters, but on the whole, it's a happy place. So, how better to add some contrast to your story then to add some morally disturbing actions to this land of joy? While this sounds to some like a horrfic idea, and is the reason we can't have nice things, to others, this is fascinating. The ones that do it right explore how thse acts of horror effect such a joyus place, and look to use that contrast to drive home greater points. Take, for example, Fallout Equestria, one of my favorite fanfictions of all time. It is a bloody, gory fic, and does not hold back. It is in total and complete contrast to the Equestria we know and love, and kkat uses that to explore friendship and morality in a much more powerful way then arguably even the show could. Done wrong, and you have stories that use it as a cheap way to illicit a reaction.
Another reason is for shock value. This is closely related to the wrong way of using contrast to tell a dark MLP fic, but different in a distinct way. While the guy who's doing it wrong for contrast is at least still trying to add credibility to the story as a piece of literature, the shock value motivation is always just for quick, cheap reactions. Done right, it can make you feel like it was terrifying or disgusting, yet odly fitting or creepy in a good way. Done wrong, and you get Cupcakes. Not eerie, not disterbing in a horrifyingly fitting way, just torture porn for no reason other then to make unsuspecting readers squirm.
Speaking of Cupcakes, another reason people write squik fic: Cupcakes' success. As parodied in RatherHomely's fic 'Terrible and Horrible Stories,' (I think, I may have gotten the fic name wrong) people write these fics in responce to the popularity of Cupcakes and related stories. Sweet Apple Massacre, Pattycake (Pretty sure I spelled that wrong. Do not care at all), Rainbow Factory, you know the type. These stories try to take some of that popularity away from Cupcakes or the like, by making it just that much worse. Some try by copying Cupcakes exactly, some try to make Sweet Apple Massacre look tame. It is here we find the worst of the worst, the stuff that makes you want to give up all faith in the fandom and just go home. No matter how well written, this stuff is always bad, no exceptions. It is gore and sex for the sake of attention and infamy, and quite frankly, I don't have to put up with it.
So, that's all of the reasons I could think of for why people would write this kind of MLP: FiM fic. I'm sure there are more, but I think they all boil down into one of these three categories at the core. I know I focused on gore rather then disturbing sex, but for that, I have to remember that YKINMK, and just not read. Then again, if it's in 120 Days of Blueblood, it is wrong and should not be allowed.