Johnny91 This feature is already added to new pending 0.9.0 release, which should be out in 4-5 weeks.
It will keep folder structure when using drag-and-drop, and create folders as required when uploading. The only downside (if you can call it that), is that you won't see the folder structure directly in the uploader interface before upload ... It will just display all files from all folders. After upload, when the page reloads, you will see the folders.