When you use ! with vi, it sends the text to the program on STDIN, and replaces it with whatever the program outputs on STDOUT. Try something like this:

#!/usr/bin/perl -w
use strict;

while (<STDIN>) {
    chomp;
    if ( ! -e ) {
        print  "#$_\n";
    } else {
        print "$_\n";
    }
}
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