At some point, your runs-as-root part needs to trust the job being submitted to it. What level of security is needed to get this trust high enough? What do you, as the SA, require the user to prove to you before you act on their request? Now, what is needed to have a program do the same thing?
Be careful about file system permissions. Perhaps run the CGI submitter under a suexec setup to allow only that CGI to touch whatever mechanism is used to pass information to run-as-root. Think "minimum privilege necessary".