taxonomy_update_7005() sometimes fails when inserting into field_data_taxonomy_vocabulary_N

Having trouble on a D6 -> D7 upgrade. Looked through all of the related bug reports / support requests on d.o, but didn't find a solution.

The error returned is:

SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry 'node-841-0-0-und' for key 'PRIMARY'

The offending insert is right here:

      // is_current column is a node ID if this revision is also current.
      if ($record->is_current) {
        db_insert($table_name)->fields($columns)->values($values)->execute();

I notice that is_current is set in this query:

SELECT td.vid AS vocab_id, td.tid, tn.nid, tn.vid, n.type, n2.created, n2.sticky, n2.nid AS is_current
FROM {taxonomy_term_data} td
INNER JOIN {taxonomy_term_node} tn ON td.tid = tn.tid
INNER JOIN {node} n ON tn.nid = n.nid
LEFT JOIN {node} n2 ON tn.vid = n2.vid
ORDER BY tn.vid, td.weight ASC, tn.tid

Running that query myself and checking the offending NID provided by the PDOexception, I see the problem is that is_current is actually flagged twice: once with the actual nid of the content, and once again for a completely unrelated node:

Possibly, my data is bad (this site went through a D5 -> D6 migration just over a year ago, possibly it's a problem with a contrib taxonomy-related module), but I think there's potentially a harmless fix. Patch attached.