Uninstalling / Reinstalling will clean things up through dropping all the tag tables and starting again.
You can also clear out the tags if you're able to run some Sql.
First you need to get all the tab modules that are 'orphaned':
select Distinct TabModuleId
from ifty_TagInstanceLInk
where not exists (select TabModuleId from dnn_TabMOdules)
Then, for each of those TabModuleId values, you can execute this stored procedure:
exec ifty_ClearTagsForTabModule portalId, tabModuleId
Substitiute in the values for portalId and TabModuleId respectively. There isn't a single 'Tag' table, the tags are stored in a complex set of interrelated tables, so you can't just delete the tags to clear them up.