Like napa said, you really need to test your code before submitting it. Anyway, your script can be written as such with a simple if-then-else statement (Yes, one if statement with && operators):

on $*:text:/^[!.](church)/Si:#:{
  if ((!%flood [ $+ [ $nick ] ]) && ($chan != #chan) && (!$exists(church.txt))) {
    set -eu3 %flood [ $+ [ $nick ] ] x
    notice $nick An error occured; I can't find the data located in my directory!
  }
  else {
    inc %church
    msg # $nick went to the $regml(1) and $read(church.txt) $+ . $&
      $nick has used this command %church $iif(%church > 1,times,time) $+ .
  }
}