I fail to see your flood protection.

var -u6 %flood flood

sets %flood for 6 seconds before it is unset and

if (!%flood) {

prevents the code from processing if %flood is $true

if ($nick !== $me)

you can simply use the ! event prefix instead of the /if
and @Master-Of-Death

on *:OPEN:?:*:{ if ($away == $true) {
.halt
.msg $nick I am away, I'll respond when I can. [amsg]
}
elseif ($away == $false) {
.msg $nick I have been idle for $duration($idle) i'll respond when I return. [amsg]
}
}

will only trigger if the person is not away, /halt stops all processing of the script so

.msg $nick I am away, I'll respond when I can. [amsg]

will never trigger.
there is no need to silince /halt either as it doesn't output anything anyways
also instead of using

if ($away == $true)

and

($away == $false)

you can shorten it with the '!' to negate it

if ($away)

and

if (!$away)