In a separate render, switching off Primary Rays for the Atmosphere shader, or even disabling it altogether, will give you a completely black Alpha for the sky all the way to the horizon, but keep the opacity of the clouds as white. If you render using the sequence tab (Render Sequence) and have Extra Output Images switched on, the Alpha will be rendered and saved automatically. Be careful not to overwrite your beauty RGB pass that has the Atmosphere intact, so use a different name for the RGB image. If the Alpha is all you need, you can dispense with raytracing, shadows, GI, etc, for a faster render.