Certainly no expert here but if you have a fairly large tree to deal with I'd imagine one could harvest in sections to lessen the damage on a tree. Assuming good root growth all around maybe dig up a third of the circular area around the tree and harvest that. Next year harvest the next third and the last third the following year. Hopefully by the time you have got to the first third section again new large roots will have grown. Also leaving permanently the roots that are directly below the trunk for good measure the tree has the possibility of survival. Hope maybe that's a decent idea.