Would it help to have some geo with the planet's curvature, at roughly the average height of the clouds, even if the clouds themselves are not represented in this geo?
You could add a Displacement Shader to a planet to displace it up to the height of the clouds. The Displacement Shader could have a Constant Scalar node as its function input, and you'd use that to set the height of the displacement.
This could then be exported to an OBJ using the Micro Exporter.
You *might* even be able to use the cloud layer's fractals to drive the opacity of the surface, if you want to get fancy, and this way you might have a simple approximation of the positions of the clouds. Micropolygons with opacities below 0.5 would be ignored by the Micro Exporter. I think...
Matt