Hmm, maybe something like this?

Code:
on *:text:*:#: {
  if ($nick isop $chan) { %spamlines = 1 }
  if ($nick == %spamnick) {
    inc %spamlines
    if (%spamlines == %spamline) { 
      msg # .timeout $nick %spamtime %spammessage
      msg # $nick you're spamming too fast. slow down!
      %spamlines = 1
    }

  }
  else {
    %spamnick = $nick
    %spamlines = 1
  }
}


This being inside the last half of the code, and I won't say it will work since I haven't tested it.

The basic idea though is you check if they're a moderator and if they are, reset %spamlines back to 1 or just unset %spamlines.