Automatically add this attribute to the gallery shortcode

You can hijack the shortcode handler and set the attribute to a value of your choice. Then call the native callback for this shortcode.

add_shortcode( 'gallery', 'file_gallery_shortcode' );

function file_gallery_shortcode( $atts )
{
    $atts['link'] = 'file';
    return gallery_shortcode( $atts );
}