Would X&Y have pokemon that have hidden motifs such as that? I mean, in the games, independent ideology is indeed possible with legendary pokemon.
Not to drive off topic, but that Togepi was more naughty and mischievous than anything else. Sure it did some pretty devious tricks, but I wouldn't go as far as call it purely evil.
In the games, there are Pokémon who have a naughty nature. But I wouldn't confuse naughty with being evil. They are very much two different natures. I don't see the games introducing an "Evil" nature into the mix, but if they did in X and Y, then I can imagine something similar to having to purify them maybe. But I still couldn't picture them being naturally born evil.