Most CGI related modules print their output so you could:

my $savedOutput;

open my $saveOutput, '>', \$savedOutput;

my $oldStdOut = select $saveOutput;

# Call CGI stuff here

select $oldStdOut;
close $saveOutput;

# process $savedOutput to clean up duplicate headers and other foibles
+ here

print $savedOutput; # Output the cleaned up CGI output text
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