To harvest roots without up rooting or killing the plant:

Imagine a circle around the plant, with the plant in the center, and extending out one to three feet (depending on the plant the roots may extend much further than this, you can follow them away from the plant as far as you need). Now divide the circle into 4 equal sections (Like cutting a pie into four peices). Roots from only one of these sections will be harvested. Start digging up the section and saving the roots that you come across. Don't dig to close to the stem/trunk of the plant. You can get pretty close but leave a couple inches. You don't want to damage the plants tap root. Your pretty much just going for lateral roots. Once you have dug out all of the roots you can find from that section than fill the hole back in. The next year you will move clockwise (or counter-clockwise doesn't really mater) to the next section and repeat this process. It should take 4-years to make it all the way around the plant. On the 5th year you would harvest the 1st section again. This allows the plant to always retain enough root system to continue growing. Trimming the roots like this usually stimulates a lot of above ground growth as well.

Edit: A plant has to be pretty mature for this to work. If it is too young it probably won't survive the first harvest.