>>I want to end up with output that is just httpd configuration directives without any Perl code left in it.

Does this work?

use strict;
use warnings;

my $configfile2parse = 'httpd.conf';
my $configfile2check = 'httpd.conf-stripped';

open FH, '<', $configfile2parse or die "cannot open httpd.conf";
   my @content          = <FH>;
close FH;

my $opener           =  qr{<Perl>};
my $closer           =  qr{</Perl>};

my @httpd_config_only = grep {!(/$opener/sg .. /$closer/sg)} @content;

open  NH, '>>', $configfile2check or die "cannot open output file";
print NH $_ for @httpd_config_only;
close NH;

my $result = qx!httpd -S -f /work/$configfile2check!;
print $result . $/;
[download]

... tests ok here - but I hope I understood your original problem correctly. Another consideration might be separating out the perl code from httpd.conf using the Include directive within the config