Why is it causing you grief?
Have you tried turning off the option labeled "Show navigation pane link in topics"?
Helpful and Handy Links
Because the security people don't like it; as it's a potential XSS Security Vulnerability.
I've turned off all the links. The page renders with no links in it at this point; stll the script is there.
We've seen this scenario before. Someone uses a tool to report security issues, fair enough. The tool then reports that webhelp is about to blow the planet to smitherines. They go back to the tool vendor and say "hey, this is standard output from RoboHelp and is not causing anyone any grief". The tool vendor then checks how their tool works and finds it is a false result. Peace ensues.
Try challenging them.
See www.grainge.org for RoboHelp and Authoring tips