Do not map (update) some fields with migrate in update action
Good news! You are doing this exactly right. By "unsetting" the fields in the source data you are taking the proper approach. This practice is common and the relative snippet of documentation is buried a bit in the Migrate Handbook:


  To use default values for NULL or '' or array() values, be sure to remove the item with unset() in your prepareRow() [or prepare()] function.


From https://www.drupal.org/node/1133448

Good luck with the migration!