The, "intent" is to protect your Mac against the flashback trojan.
If you think your Mac is infected with the flashback trojan, then you need to install this update > Java for Mac OS X 10.6 Update 8
You should install that update to be on the safe side regardless of whether or not you have Java enabled in Safari > Preferences - Security.
It's relatively easy and only takes a few minutes.
Keeping your Mac OS X software up to date is the best defense against malware.
I have scanned my system a few times over the last month, and nothing is ever found.
If you are runnnig a/v software, it's doubtful it would locate the files and even if it did, it wouldn't remove them.