Is there a way to get rid of the minimize button when the window is maximized? I've already gone into gconf-editor /apps/metacity/general/button_layout and changed "close,minimize,maximize" to "close,maximize" but that doesn't affect the buttons when windows are maximized.
No; Unity does not support customizing the layout of the buttons in the panel.
If you use Ubuntu 12.04, go to the
Navigate to org -> gnome -> desktop -> wm -> preferences and in the right-hand-side panel select button-layout, remove minimize and press Enter.
Then your minimize button must be disappeared. Is that what you mean?