Is there a way to untaint html documents downloaded from the Internet
To fully clean the file, you need to remove the two extended attributes that are used to mark it as a quarantined download, and track where it came from:
xattr -d com.apple.quarantine file-to-clean
xattr -d com.apple.metadata:kMDItemWhereFroms file-to-clean
To save typing and/or typos, you may want to wrap this in a simple shell script...
Remove the verified download plugin located in your /Library/Internet Plug-Ins folder.
I use FlashGot + Speed Download in Firefox and haven't had to deal with those warnings.