What's funny is that, when you really look at it, MLP was FAR more violent than G.I. Joe in the fact the characters actually came closer to death more than the Joes/Cobras with their inability to aim properly:
MLP: The Movie: A trio of witches flood Dream Valley with a purple ooze that comes close, more than once, to actually drowning/suffocating them.
The Ghost of Paradise Estate: Dream Valley is flooded, this time with actual water, by a monster squid with a powerful amulet. There's no telling how much wildlife drowned in the chaos.
The End of Flutter Valley: The witches return to wipe out neighboring Flutter Valley, enlisting mutant bees this time. One pony is nearly gored by a rampaging bull; A massive forest fire nearly wipes out the Flutter Ponies; Several others are nearly dropped off of a rope bridge.
The Glass Princess: A pig princess transforms all of Dream Valley into glass, including it's inhabitants. The ending of part 3's really creepy in that aspect.
Bright Lights: A shadow stealing cloud threatens everything, leaving his victims essentially weak and, in some cases, zombie like.
Return of Tambelon: A demon ram tries to banish everyone to an interdimensional void, as well as making the human kids his personal slaves. Oh, and his armies have weapons, even if they aren't really *lethal*.
The Magic Coins: Once again, the heroes are nearly tossed off a suspension bridge; Another forest fire tears through the valley; A good amount of characters nearly die from dehydration; more wildlife is possibly killed in a drough/forest fire.
Baby it's Cold Outside: Mutant Penguin freezes over the world; Turns a few characters into ice statues, but are later seen to be okay; Lots of creatures possibly killed by frostbite.
Crunch the Rockdog: Giant stone pitbull rampages across the land, turning everything into stone. Oh, and the moral of the story is that 'It's alright to hide your emotions'.
Quest of the Princess Ponies: Lava Demon threatens to flood the land with, you guessed it, lava. Once again, lots of creatures possibly killed offscreen in the flood.
Sonambula: Youth stealing witch sucks the life out of several ponies. Potential incest is implied when the Big Brother Ponies arrive.