Turns out I wasn’t far from the answer:
function mce_mod( $init ) {
$init['apply_source_formatting'] = false;
return $init;
}
add_filter('tiny_mce_before_init', 'mce_mod', 99);
add this to functions.php and it will stop the nbsp’s.
if you want to fully tame tinyMCE I recommend you check out this gist