Its a good idea to warn users what they are opening but this is a pain if the an archive is opened but then you want to move it somewhere else that isn't using typical OS X apps that understand and can clear this perm. (like unix dev location under webserver).
I've found this xattr command to work to clear out that problem:
xattr -d -r com.apple.quarantine directory
It will verbose blurb out stuff but at least it gets rid of it and allows reading of those files by various unix programs (like apache).