That's because # is the same as $chan, try this:

Code:
alias channelkill {
  if ($left($1,1) !== [color:red]$([/color]#[color:red],)[/color]) {
    echo -a Channel Kill Error: First parameter is to be a channel!
  }
  elseif ($2 == $null) {
    echo -a Channel Kill Error: Second parameter must be filled with a reason!
  }
  else {
    echo -a Channel Kill Command Success
  }
}