The "Save the Cat" series of books on screenwriting says that's an essential part of such movies - that the monster only gets to invade because someone's moral failing lets it in.

I'm not fond of their attitude - that there are only about a dozen possible plots for movies - but there certainly are a lot of movies that conform to them.

A Wrinkle in Time?

Good question. As I recall, I found the first half much more interesting than the last half. In retrospect, I think that one reason was that the Ws required thought to understand but It did not. (But I don't recall thinking this at the time, so take that with a grain of salt.)

Charlie and the Chocolate Factory […] Alice in Wonderland

The morality in these is farcical, so it's easier to be grey, or just meaningless. (In Tim Burton's recent adaptation of Alice, which has a coherent plot unlike the original, the morality was very black and white.)

Now I remember the famous debate in The Horn Book Magazine about the morality in Charlie. I found most of that debate pointless because Charlie's morality is farcical, so why would you expect it to make sense? (Well, the debate wasn't only about morality.)

And that reminds me of Ursula Le Guin (who took the anti-Charlie position in the first April 1973 Letter to the Editor at the above link); she wrote the children's fantasy trilogy Earthsea. This has a fairly grey morality, especially the middle book, which is told from the perspective of an antagonist (at first) of the trilogy's main protagonist. Years later, Le Guin wrote a sequel trilogy, which (while earning a mixed reaction from the fans) addressed some of the problems that she saw in the original trilogy; it was even greyer, but it was not marketed to children anymore. In any case, Earthsea is not a counterexample to ewbrownv's claims, because the story does explore ‘unconventional morality, novel social forms, etc’ (and does it well, IMO).

Ob MoR: Earthsea has an anti-lifeist moral, but because it is grey, it treats the lifeist position with some respect; the villains are more misguided than evil, and you can sympathise with them. Lifeists still won't be happy with it, especially in the sequels, where gur urebrf qrfgebl gur nsgreyvsr (although once you get to that point, this is pretty well justified). But at least the lifeist position is not dismissed out of hand.

Are you asking for children's literature, or YA?

The younger the better, I suppose. Although library and bookseller classifications have to draw the line somewhere, there's really a continuum of target audience ages. Anything that is widely read by children should count, regardless of how it's classified (although how it's classified may give a reasonable estimate of whether children read it, in the absence of real data).

Eliezer has referred to HP as ‘for children’ when explaining some of the changes that MoR (which is not for children) has to the background universe. But HP is often classified as YA. I would not want to be picky.

humanizing a villain that would predate on someone that young would not be wise.

That's an interesting argument. I definitely believe that children must learn that villains are humans too by the time they are old enough to commit acts of revenge that can cause significant harm. So certainly tweens (who will soon be old enough to join gangs, plan for future careers, etc) should read about humanized villains, while still reading about heroes who resist them. But very young children may need to classify people strictly into good and evil to successfully avoid harmful people. That's an uncomfortable idea to me, but I don't know enough about child psychology to rationally evaluate it.