Well, I don't use Nessus 3, but the older Nessus 2, which still is free software, and not just freeware, and is available in the Fedora-repos.
But, long talk short, I found that /etc/nessus/nessusd.conf (your location might be different, probably somewhere under /opt) holds the setting safe_checks = yes, which, when set to no should do what you are looking for.
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