I suppose you could use on input to catch it.
Code:
on *:input:*: {
  ; this will catch and stop someone from accidently doing something like msg instead of /msg in a channel window
  ; which i assume is the purpose of the request.  Change/Add IF's to make it more or less strict.
  if ((msg isin $1) && (serv isin $2)) {
    if ($active != @YourCustomWindow) {
      echo $color(info) -eati * You must enter services commands in the dedicated window!
      HALT
    }
  }
}