No, unfortunately when figure() is used to activate a figure or to create a new figure, it is always going to be raised to the top.
Sometimes you can get away with
set(0, 'DefaultFigureVisible', 'off')
but that probably would not work with export_fig.
Sometimes you can get away with running MATLAB with -nodesktop and doing the graphing and saving without the graphs being enabled. That can depend upon the graphics features you use and upon the kind of file you are saving to.