I am working on Chilipeppr Eagle widget board mirroring. You can try it here: http://chilipeppr.com/mfb
Still in progress, but it looks the gcode for Top/Bottom is generated properly. So with some manual gcode file manipulation (to remove unneeded gcode parts) it is possible to mill two-sided boards. Just choose Top or Bottom layer from the dropdown list, keep ‘Mirror this layer’ unchecked and you will generate gcode.
I think its time to talk to @raykholo and @jlauer now and discuss some functional details of the mirroring feature.