There is some reason to keep the <pre> tags around and I think you just bring it up the good reasons for it. One feature distincts both tags is download link. With <code> tags, the part surrounded is downloadable.

With <code>

#!/usr/bin/perl

use strict;
use warnings;
use DBI;

# code following
__END__
[download]

With <pre>

#!/usr/bin/perl

use strict;    # don't ever write
use warnings;  # without strictures
use DBI;

# code following
__END__