Recently I have seen a friend's website considered as malware by Google. An sql injection caused the problem.

How can I set up my webserver in a way where it scans all the websites / sqls and alert me for any abuse. What are my options here ?

You want a warning if something gets abused? Or whether or not SQLi is possible at all (scanning for vulnerabilities)?

For the first perhaps http://www.modsecurity.org/ can help you out. For the last I'd look ito SQLmap/Nikto