Drush pm-download removing the destination folder
This sort of request is best made in the issue queue, since what you are requesting is a change in behavior in Drush.  The default behavior for pm-download is to always provide a clean unaltered copy of the module; I for one would be reluctant to alter this behavior, but I could potentially get behind a new option that introduced 'merge' behavior.

A better option, I think, would be for you to download Drupal to a temporary folder, and do the merge yourself in your script as a secondary step.