When an application has been written to run as root, the Security Administrator role has three options (all of which should be assessed for consistency with the site's security policy):
If a real UID of root is not required, set up the application to run with an effective UID of root.
Otherwise, set it up with a real UID of root.
Find out what privileges the application needs and assign only the needed privileges, after determining that the application can use the privileges in a trustworthy manner.