The items outside the editor widget are controlled by your desktop theme, so if your desktop isn't dark, neither is that part of Geany.
Although I agree with you that letting random external themes mess with your applications look and feel is a bad idea, the powers that be have determined that its more important that the application looks like the rest of the desktop than it be internally consistent, so this will not change.
But GTK does give you a means of setting individual styles for applications, see the manual.