it's not spite. She didn't "sink" it because she was spiteful, she wanted to say something about the films and her work and chose to deconstruct the act of making a sequel to a trilogy after 20 years. It's their art, they can do what they want with it.
Their work since Matrix has always been avant-guard (Cloud Atlas is barely a film in any normal sense, a Speed Racer film by anyone else isn't _that_) they were never coming back to make another stock science-fiction action film.
The real question is, how did Warner green-light the script and release knowing that it was going say all those things.