Maybe I'm dumb but I still don't get it. I don't see how current can flow from ground, to the output, unless its input power is removed and the output has a load with a ground lower than the ground of the converter. Perhaps a schematic of your setup - not the specifics of the converter, just the modules/blocks you're connecting. If the input power isn't removed, and the chip is disabled, then current still won't flow through the body diode, because it will be reverse biased.
It really does sound like you want to disconnect the load, in which case the body diode isn't involved, because if there is power to the input, and the chip is disabled (EN - low) current will flow through the inductor, then diode, to the output. A common way to do that is to use a PMOS driven by an NPN, which in turn is driven by the EN signal. When EN is high, the NPN conducts, turning on the PMOS on the output.