Cannot redeclare backup_migrate_drush_command()

Somewhat obscure use case.
I have some sites on multisite with a shared codebase in sites/all/modules/. I sometimes use a site example.com to test dev modules. I deactivate the module for that site, install the dev module in sites/example.com/modules/ and activate it again.
When I do this for backup_migrate-6.x-2.x-dev, having disabled backup_migrate 6.x-2.2 for this site, but having it still physically existing in the shared codebase at sites/all/modules/ to cater for the other sites, drush gives me the following error warning on subsequent commands:

Fatal error: Cannot redeclare backup_migrate_drush_command() (previously declared in /codebase/sites/all/modules/backup_migrate/includes/backup_migrate.drush.inc:15) in /example.com/sites/example.com/modules/backup_migrate/includes/backup_migrate.drush.inc on line 57
Drush command could not be completed.

Drupal itself allows the dev instance of backup_migrate to override the instance in the shared codebase because it is more specific to example.com.
I would also expect a similar mechanism for drush integration. Should i port this question to the drush queue?