I understand what you're saying, but you still can't halt it entirly...

Code:
on 1:CONNECT: {
  /newver mIRC $version Khaled Mardam-Bey (KingTomato Test)
}

alias newver {
  /set %vers $1
  .debug -ni @d- $+ $cid newVersion
  .window -nh @d- $+ $cid
}

alias newVersion {
  /tokenize 32 $1
  if ((*!*@* iswm $2) && ($5 == :VERSION)) {
    var %nick = $right($gettok($2, 1, $asc(!)), -1), %addy = $1
    .ctcpreply %nick VERSION Boo
    /halt
  }
  return $1-
}


//ctcp $me Version

Returns:

[22:49:35] -> [KingTomato] VERSION
-
[22:49:35] [KingTomato VERSION]
-
[22:49:35] [KingTomato VERSION reply]: mIRC 6.12 Khaled Mardam-Bey (KingTomato Test)
-
[22:49:36] [KingTomato VERSION reply]: mIRC v6.12 Khaled Mardam-Bey


You still get the default msg..

-KingTomato