How can I delete taxonomy terms for a specific node type?
The field isn't part of the type, but the terms remain assigned to the existing nodes. 


That doesn't sound right; to the best of my knowledge removing the field from a content type will (normally) remove all data attached to nodes of that type. They get moved to a field_deleted_* table and then purged on a cron job. 

It might indicate there's a problem somewhere in your installation, or it might just be 'one of those things'. 

The 3 tables you mentioned are the only places you'll need to delete data from, but you'll also need to flush the caches after the purge (or at least truncate cache_field)