Most depth of field (DoF) calculations are based on the assumption that the image will be viewed as an 8X10 print at a viewing distance of about 10 inches (25cm) by a person with 20/20 vision. For a 35mm film sized image, that means about an 8X magnification factor. For a blur circle to be perceived as a point at that display size and viewing distance, it must be about .03mm or smaller on the unmagnified virtual image projected by the lens onto the recording medium (the film negative or the digital sensor). Zeiss assumed that some people viewing the photo would have better than 20/20 vision and allowed for that in their calculations to arrive at .025mm. In either case, the allowable CoC for viewing an 8X10 print at 10 inches is several pixel widths wide. In the case of the Canon 5D mark II, both .03 and .025 are between 4 and 5 pixels wide.
If you are pixel peeping at 100%, then you are viewing the image at a much greater magnification than the 8X10 standard. You are viewing it at around 45X magnification, so areas of the image that appear sharp at 8X magnification are revealed to be slightly blurry at 45X magnification. In this case, you would need to use the pixel pitch of the sensor for your circle of confusion when computing what the DoF would be for that viewing condition.
With digital sensors, the size of the pixel determines the size at which the circle of confusion (CoC) becomes significant when viewing at 100% crops. Any blur circle smaller than the pixel pitch will be recorded as a single pixel. Only when the blur circle becomes larger than an individual pixel will it be recorded by two adjacent pixels.
The other thing to consider is that each pixel on your sensor is only sensitive to either Red, Green, or Blue. To produce a color image either your camera's jpeg engine or your RAW conversion software applies a demosaicing algorithm to produce a seperate R, G, & B value for each pixel using complex mathematical interpolation. This demosaiced image can then be sharpened by software that uses contrast between adjacent pixels to try and reclaim some of that lost resolution. That is why .007mm is probably close enough to the .00639 pixel pitch of the 5DII's sensor to use in calculating the DoF when viewing at 100%.
Here is another way to look at it. If you have a monitor with a resolution of 1920x1080 and you display an uncropped image from your 5D II on it, each pixel of you monitor is combining between 3 and 4 pixels worth of data from your camera into each pixel. Any part of the original image that is blurred by less than 3 pixels will appear just as sharp on your computer monitor as the sharpest part of the picture. But when you magnify the picture to 100% and only look at part of the image filling your entire screen, you will be able to see any blur that is greater than 1 pixel wide (assuming your vision is good enough and you are close enough to see individual pixels).