Perhaps they would like to give you more control and avoid problems caused by deleting the MP6 plugin, such as losing the modification to the php/css/… files of MP6 by your own.
No worries. The upgrade process (see wp-admin/includes/upgrade.php) will “Deactivate MP6 on update to 3.8.” See github.com/WordPress/WordPress/commit/8b8c8e96e7f3cb67f0c8ae18541a7a1b6fe3a96b
