I agree, leave it, because the roots will be a problem.
'Green Giant' has normal growth pattern for Thuja occidentalis. It grows rapidly, and is somewhat coarse in branching. It is a cultivar that keeps a green color over winter. The the typical forms of Thuja will ''bronze out'' for winter. The foliage will change to a bronze-purple or brown color, then return to green once growth resumes in spring. 'Green Giant' does not change color.
So for bonsai the forms of Thuja occidentalis with normal growth pattern are probably best for medium to larger size bonsai trees. Their cousin, Hinoki, is good for medium to smaller size bonsai.