Updating taxonomy terms with vbo and workbench
The basic principle behind using Views to display the latest revision, instead of the published revision, is to base the view on the node_revision table instead of the node table. Unfortunately you cannot change the base table of an existing view, so you'll have to rebuild the entire view showing "Content revisions" instead of "Content".

To display only the current revision, use the filter criteria "Workbench Moderation: Current" on the node_revision table (otherwise all revisions will be displayed). To gain access to fields on the node itself, add a Relationship of "Workbench Moderation: Node" (and then be really careful you don't use this relationship unless you intend to reference the published node).

To avoid a potential security bypass in your view, you should also include the filter criteria "Content access: Access" on the Node relationship.

With all that plumbing out of the way, you should now be able to edit the taxonomy term field on the most recent revision of your nodes using "Content (historical data): [taxonomy field name]".