That was indeed rather dark when you think about it. Disney movies do indeed have a layer of darkness. The hunchback of Notre dame had one of the most twisted villians of any disney movie i have seen! (And I have probably seen them all from before 2009!)
Speaking of darkness, Don bluth movies in general seem to be like disney, only even gloomier in general. All dogs go to heaven, Titan A.E, even the land before time had its moments of gloominess. Titan A.E has to be my favorite bluth movie, and if I recall, it was his last as well, before he shuttered his studio. the last one especially, being about the last survivors from earth after the end of the world, and are now drifters out in junky spaceships looking for a home.
Another kinda dark show, well in a way, is ed, Edd, n Eddy. When you think about it, hardly anything goes right for the ed boys, they always got stuck in some crazy way, usually done either by the cul-de-sac kids, or the kankers, in their crazy obsession for them . not very dark, but kinda sociopathic humor considering its humor is mostly derived from the misfortune the ed boys get.
Courage the Cowardly dog, full stop. so many psychotic creatures, the bangs and courage never could go anywhere without encountering a homicidal lunatic, heck, they couldn't even stay at home without doing the same!