I'd use a ban not a kick only, you are liable to find yourself disconecting for excess flood or continually kicking people over and over if they have rejoin chan when kicked enabled (3 or 4 sets of clones joining will leave you kick flooding forever).

using SladeKraven's code + a 20 second ban to stop them rejoining

Code:
 
alias clone {
  if ($ial == $false) { 
    .ial on
  }  
  if ($chan($chan).ial == $false) { 
    who $chan 
    return 
  }
  if ($ialchan($wildsite,$chan,0) >= 3) {
    ban -u20 $chan $nick
    kick $chan $nick Clone nicks exceeded.
  }
}

On @*:Join:#YourChannelName: {
  clone
}