I am a microdrive user with a D2x. I don't know about reliability with the Canon (hopefully they can fix the problem), from what I've read the problem is with some brands/types of CF cards also.
But the question to me is can the drive keep up. The uber cameras have sizable buffers and if your shooting rate is typical, then effectively my microdrives are the same as a fast CF card. The additional speed of the CF card is wasted in my usage. If your a sports shooter, or equivalent, then the fast card dumps the buffer faster and will allow the camera to keep up. Landscape/wildlife is rarely fast shooting so you will likely never know the difference.
I have yet to experience any holdup due to using a microdrive, but then I don't hammer 30 shoots with the shutter release held down. If you need speed then the fastest card is where you want to be (Extreme III), a slower CF card is just a bandaid (II).