You are better off doing this at the hardware level. That way, you don't have to worry about making the firmware setting whenever you reset your firmware settings.
However, this is easily done from the firmware level. Just use RepG 40r30 - Sailfish (a download of this thing). In RepG, select the correct machine type (Machine > Machine type (driver) > Replicator 1 Dual (Sailfish). Then connect over USB. Then in RepG select Machine > Onboard Parameters. In the popup window invert the setting for the Y axis on the tab with the axis direction and endstop settings. Then commit the changes.