You can delete a tree that is not associated with collection objects by deleting the top node of the tree (typically Kingdom). Right-mouse-click on the top node and you are given a dialog of options. Delete will be available if there are no associations to collection objects.
If you do have associations between your collection objects (specimens) and tree taxonomy nodes, then deleting the tree nodes will delete these associations and you would need to re-establish them. You should proceed with caution and consider your options. We appreciate your apprehension in working with MySQL if you are not familiar with databases. If you do not have access to IT support our engineers are happy to assist you through our Data Cleanup Management services. We are happy to discuss your situation with you.