The person asked if you could disconnect the amp in order to defeat the factory amp and get rid of the distortion(or at least that was my understanding). You cannot just unplug the amp and still have sound. you must as You say:
and tap into those wires from the new after market HU
This is far from just disconnecting the plug. It might have taken you 5 mins to disconnect the plug, but I highly doubt it took you 5 mins to locate the correct wires and properly connect them.
I have bypassed my own rf amp and understand exactly what you mean.