She said she would deal with the Heartless, so I guess it can't be said she died from them, I guess. She also said (during Hollow Bastion) "I'll take care of the White Ones. You leave and find a way to vanquish them forever!" instead, she got "dogpiled" by the Dusks and vanished.
As for the villian returning, I hated Malificent's return mostly since they didn't really explain how she went from a stain in Hollow Bastion to Twilight Town, inside Yen Sid's tower. There wasn't any explanation except for her crow (which hardly appeared in KH) carrying her robe to the Three Good Faries; at which point, they said "Gee, I wonder who that belongs to?"
"*Gasp*! Mali-"
"No, no! We mustn't remember her name!"
"...She was a mean, old witch!"
"Oh, no! the memories are coming back! What will we do?! What will we do?!"
"MALIFICENT!!!" All 3 faries disappeared, as did Yen Sid. Malificent then stood, and laughed... like a hag.
Come to think of it, Ursula was even worse. She just came back from the dead for no reason, and nobody acted surprised.