Add an option in the settings from Amarok, to close the application completely when an user close the main window from Amarok and don't stay in System Tray. It,s IMHO a bad design when an user space application don't close itself completely when an user click the close button (raise the Xorg destroy window event). Amarok is NOT a required system service.
There already is an option Settings -> Configure Amarok ... -> General -> Show tray icon Also nothing in my systray is a required system service and I think it's a valid choice to be shown state there or easily interact with an application that is hidden/on another desktop/whatever.