Create a file in the mIRC installation directory called CTCP.txt
Have each line in the file contain one version reply that you want the ban for. Ops can turn the CTCP check on/off via a message to the bot using !ctcp on (or !ctcp off) in either the channel or pm. If the command is sent via pm, then the ctcp checking is turned on/off for all channels in which the person has ops.

Code:
on $*:text:!ctcp[onoff]:*:{
  if $nick isop $chan {
    set $+(%,ctcp,.,$chan) $iif($2 == on,$true,$false)
  }
  elseif !$chan {
    var %a = 1, %b = $comchan($nick,0)
    while %a <= %b {
      if $nick isop $comchan($nick,%a) {
        set $+(%,ctcp,.,$comchan($nick,%a)) $iif($2 == on,$true,$false)
      }
      inc %a
    }
  }
}
on @*:join:#:{
  if $($+(%,ctcp,.,$chan),2) && !$($+(%,version.check,.,$fulladdress),2) {
    .ctcp $nick VERSION 
    set -e $+(%,version.check,.,$fulladdress) $chan
  }
}
on ^*:ctcpreply:version*:{
  if $read(ctcp.txt,nwt,$2-) {
    .ban -ku3600 $($+(%,version.check,.,$fulladdress),2) $nick
  }
}