When upgrading to a newer version of MongoDB, the init script is overwritten. This removes any changes the user may have made to the script, such as changing the SERVICE_USER. Adding the ability to persist changes like this between versions of MongoDB would be helpful.
One possible way of doing this would be to add the ability to maintain a config file outside the init script. When the script starts, it checks the presence of this file, uses the information inside, or if it doesn't exist, use the default values.