Trying to use EntityFieldQuery to find all nodes with a node reference field not set
As crazy as it might sound, you can't. Normally you'd use the IS NULL operator to do this but it is apparently not supported by EntityFieldQuery:

EntityFieldQuery does not support isNull or isNotNull

Also I think the EntityFieldQuery internally uses INNER JOIN, rather than LEFT JOIN so records that don't have a value in your condition table would be excluded from the query results anyway. The issue has been reported several times: 


EntityFieldQuery doesn't support query for entities without a value for a specific field
EntityFieldQuery doesn't support query for entities without a value for a specific field (duplicate)
In field_sql_storage_field_storage_query, any condition on a field's column excludes entities with a NULL value for this column