1. Marvel Studios is a self contained entity, they're just like Pixar Disney lets them do their own thing for the most part.
2. The Disney doesn't want Marvel to go dark is unsubstantiated fanboy BS. If Marvel wants to do something with their more darker characters, they'll do them. They don't need to $100 million movies, nor should they and Marvel has said they want to go do smaller B/C-list characters after the Avengers. Also as bad as the PotC sequels were, they got pretty dark especially for a Disney movie. I mean the third one opened with a kid getting hanged, and if I remember correctly a Chinese prostitute getting shot in the head.