Bearaway
You are asking the right questions and the specs of the 5D2 are a little misleading. The bit rate is high but the sensor sampling is done rather poorly, resulting in aliasing artifacts which causes the Digic IV encoder to lose a lot of detail, even at such a high bitrate. With all the compression bandwidth the 40+mbps gives, junk in junk out, well not exactly junk but you get what I mean.
What does this all mean? The compression artifacts from the aliasing can be pretty bad with a sharp lens and deep DOF. I think one of the reasons why every loves the 5D2 is because the drawbacks of the sampling actually enhances the qualities which many people like, false detail that people see as "sharpness" when it's just aliasing. If you look carefully, there is less detail in the image. People with wrinkles love this camera.

That's the biggest reason why BBC won't even consider this a B cam even. However, there are other broadcasters who would, as can been seen by various TV and even one film project I know which is using the 5D2. The super sharp fast lenses, low noise and DOF control are the reasons why it's popular topside.
As for workflow, yes transcoding is needed to be efficient. ProRes, DNxHD, Cineform and Canopus all work the same way. A normal computer with 4-8 cores would do transcoding at 1-1.7x realtime using CPU with OpenGL GPU acceleration. nVIDIA CUDA GPUs like the FX4800 or Quadro CX go even faster, about 30-40% improvement in performance.
Hopefully in the October shootout of the 5D2 housings I'm planning, we'll cover some of the more technical stuff.