If the incoming post through xml-rpc contains a custom field 'URL', set the post format to 'link'.

post2linkpost.php

<?php

// Add to functions.php

add_action('save_post', 'rei_xmlrpc_process_post');

function rei_xmlrpc_process_post($post_id)
{
    if (defined('XMLRPC_REQUEST') && XMLRPC_REQUEST)
    {
        $post = get_post_custom($post_id);
        if(!empty($post['URL']))
        {
            set_post_format($post_id,'link');
        }
    }
}
?>