Untagging a file or another object is as simple as deleting it. Don't worry: an object is actually deleted from Tagsistant only when it's removed from the last tag. As an example consider this situation:
$ cp /some/file.txt ~/myfiles/docs/texts/@/
$ rm ~/myfiles/docs/@/file.txt
Here file.txt has been untagged from docs but it's still recorded in the database and tagged as texts.
To delete a tag just remove it from the tags/ directory:
$ rmdir ~/myfiles/useless_tag/
Please be careful: never remove anything recursively from the tags/ directory! Since the tags can be combined in any permutation, a recursive deletion will explore all the available tags and delete everything inside. That basically means that your entire filesystem will be emptied! This is also the reason why deleting a tag from a filemanager could prove to be impossible. Future releases of Tagsistant will introduce a new directory for tag management where tags will feature without their content to ease tag deletion.