If you render without atmosphere (either by disabling the atmosphere completely or just disabling "primary" on the atmosphere), your clouds RGB and alpha should be correct for compositing with other images using the "over" composite operation which is pretty standard for compositing CG elements. The clouds will be premultiplied by the alpha, but that's what you should have. Can you show me an example of how it doesn't look right?
If you're compositing using some other mode and you really need to unpremultiply, you could try dividing the RGB by the alpha image, but that might not be very reliable.
(BTW, the reason the alpha images produced by default include a blue sky is because they include the "spectral alpha" of the atmosphere, so that you can composite the atmosphere as well as the clouds.)
Matt