Yeah, I get annoyed by that too. You can hide the GUI (either within code or on the command line) with
set(myGuiFigureHandle, 'Visible', 'off')
and restore it with
set(myGuiFigureHandle, 'Visible', 'on')
which is fine in some situations, but not if the user simply wants to minimize for the time being. You could detect a minimize and hide, but then the figure window will disappear from the task bar, and the only way to restore its visibility is from code or the command line.