Instead of modifying the plugin every time it is updated, I’d recommend to make the modification in the theme instead.
By adding a few lines of code to the functions.php in the theme, it is possible to remove the wrong shortcode and replace it with the SoundCloud Is Golden version:
if(function_exists('soundcloud_is_gold_shortcode')) {
remove_shortcode('soundcloud');
add_shortcode('soundcloud', 'soundcloud_is_gold_shortcode');
}
It might be preferable to has it added as an action instead, but I couldn’t figure out which action hook to use.
Edit:
Apparantly the HTML5 embed has been implemented in Jetpack, but it requires the user to enable the feature in the profile settings here:
https://soundcloud.com/settings/extra
Though, to have both plugins working at the same time it is still necessary to make the modification above.