Just so you know...
McAfee also throws up a serious warning, giving me the following information:
Potential Malicious ANI File Detected,
Exploit-ANIfile.c
Potential Unsafe Script Detected,
JS/Exploit-BO.gen
Seems like these are all proactive types of warnings/protections, there are very few actual exploits in the wild for the types of operating system vulnerabilities being detected. However, I would remove the offending files/scripts as it will deter people from visiting your site.
-Danny