This must have flown under the radar, because I haven't heard anything about it and people have been complaining about this since the beginning of time. It looks like Canon actually enabled a true "Auto ISO" feature with the new firmware update in the 5D MKII, but you need to have Live View and movie mode enabled to access it in still photos.
Read below:
Among other things, this update adds manual control of ISO, apertures, and shutter speeds in movie mode. The adjustment range for each setting is as follows:
ISO: 100 – 6400 (12800 with ISO Expansion)
Shutter Speeds: 1/30 – 1/4000 in ½ or 1/3 EV increments
Aperture Values: According to lens (no restrictions)
Here are some tips for making the most of this new manual control:
• With this update, Auto ISO is fully functional (i.e., ISO values vary automatically as per the chart above) in manual mode for still photos* captured during movies or in Live View mode as well as video recording with the 5D Mark II. This can come in handy when you want to maintain correct exposure in changing light conditions with the shutter speed and aperture manually set. If you want to try Auto ISO for stills or movies, be sure to pick a shutter speed and aperture combo that's appropriate for the lighting conditions at hand.
• Although it is now possible to select wide apertures in any lighting condition, you may find that high shutter speeds can cause a "staccato" effect to moving subjects. ND filters are still very useful in bright light for this reason.
• Consider setting the shutter speed to approximately 1/50 to achieve a more "filmic" effect for video recordings with the 5D Mark II camera.
• Consider setting the camera's exposure level increments to the default 1/3 steps for finer control. (Custom Function I-1.)
• Consider the use of Highlight Tone Priority (Custom Function II-3-1) to preserve more highlight detail, especially in high-key or wide dynamic range shooting conditions.
*The EOS 5D Mark II must be set to Live View/Still + Movie/Movie Display in order to access variable Auto ISO in the camera's Manual mode. When Live View is off, Auto ISO is locked in at ISO 400 in the 5D Mark II's Manual mode.
ISO: 100 – 6400 (12800 with ISO Expansion)
Shutter Speeds: 1/30 – 1/4000 in ½ or 1/3 EV increments
Aperture Values: According to lens (no restrictions)
Here are some tips for making the most of this new manual control:
• With this update, Auto ISO is fully functional (i.e., ISO values vary automatically as per the chart above) in manual mode for still photos* captured during movies or in Live View mode as well as video recording with the 5D Mark II. This can come in handy when you want to maintain correct exposure in changing light conditions with the shutter speed and aperture manually set. If you want to try Auto ISO for stills or movies, be sure to pick a shutter speed and aperture combo that's appropriate for the lighting conditions at hand.
• Although it is now possible to select wide apertures in any lighting condition, you may find that high shutter speeds can cause a "staccato" effect to moving subjects. ND filters are still very useful in bright light for this reason.
• Consider setting the shutter speed to approximately 1/50 to achieve a more "filmic" effect for video recordings with the 5D Mark II camera.
• Consider setting the camera's exposure level increments to the default 1/3 steps for finer control. (Custom Function I-1.)
• Consider the use of Highlight Tone Priority (Custom Function II-3-1) to preserve more highlight detail, especially in high-key or wide dynamic range shooting conditions.
*The EOS 5D Mark II must be set to Live View/Still + Movie/Movie Display in order to access variable Auto ISO in the camera's Manual mode. When Live View is off, Auto ISO is locked in at ISO 400 in the 5D Mark II's Manual mode.
From: http://digitaljournalist.org/issue0906/tech-tips.html
Seems like it would be easy for them to make this possible with regular, non-Live View shooting. Maybe the next firmware update? 
