article.php

<?php
// article.php located at /themes/<theme>/article.php
// ...

// replace
echo article_markdown();

// with
echo custom_markdown();
// ...
?>

functions.php

<?php
// functions.php located at /themes/<theme>/functions.php
// ...
function custom_markdown() {
    // if you just want the raw content you saved
    $post = new Markdown;
    $post = $post->transform(Registry::prop('article', 'html'));
    
    // Create new matching function
    function _handle_match($match) {
        // Requires pre and code tag to be both on the same line for this to work
        return '<pre'.$match[1].'><code'.$match[2].'>'.htmlspecialchars($match[3]).'</code></pre>';
    }
    // Encode whatever's in the <pre><code> to special characters
    $post = preg_replace_callback('/<pre(.+?)><code(.+?)>(.+?)<\/code><\/pre>/s', '_handle_match', $post);
    
    // Output converted post
    return $post;
}
// ...
?>