movies with 'happy endings' that are really fucked up when you think on them

Yeah

Some people don’t like but…

To me it’s a dreadlock holiday situation

Bigger Than Life (1956): James Mason must either give up the drug that saved his life, or find a way to live with said drug's side effects (which nearly destroyed his family).

Possibly does not count, because director Ray has to have known this was a terrible set of options.

In Scrooged the ghost of a homeless person who froze to death cheers because his death facilitated a yuppie experiencing an almost completely incoherent revelation about the meaning of Christmas

about as happy as you can expect from a Michael O'Donoghue script

Dune (1984)

from Wikipedia: Paul demonstrates his newfound powers and fulfills the Fremen prophecy by causing rain to fall on Arrakis.

however there's a tiny problem with that: it kills the sandworms, ending spice production because the sandworms are integral to that, ends practical interstellar travel, and effectively causes the collapse of human civilisation

re ET, AI, Dune, I wonder who would win in a three-way shootout of movies with ostensibly happy but fucked up endings between Spielberg, Kubrick, and Lynch?

Nicole Kidman telling Tom Cruise, "Git yer boots on cowboy, it's humpy pumpy time!" feels like a top contender...

the parents in Time Bandits sucked, so them getting vaporized and Kevin being free to do whatever he feels like IS a happy ending, we loved it as kids