How about changing /etc/init.d/freshclam
to check if values are being set, before adding them to config file, at least for those which else produce errors when the config is parsed?
[ -n "$ExtraDatabase" ] && echo "ExtraDatabase $ExtraDatabase"
[ -n "$PrivateMirror" ] && echo "PrivateMirror $PrivateMirror"
[ -n "$ExcludeDatabase" ] && echo "ExcludeDatabase $ExcludeDatabase"
[ -n "$DatabaseCustomURL" ] && echo "DatabaseCustomURL $DatabaseCustomURL"