|on Dec 16, 2012 at 14:53 UTC||Need Help??|
IMHO, you should be doing something to fix the problem;
Check the logs, close the exposure holes, etc. Then fix the code and don't let it happen again.
I've been hacked, and it isn't fun, but I fixed the source of the problem.
To answer your question, a very simple Perl script run every hour could check the modified JS to a checksum and if it fails to verify, then notify the sysadmin. But if the site is that un-secure, then maybe *they* could modify your Perl script!
"Well done is better than well said." - Benjamin Franklin