Adding nofollow via Javascript is redundant as just about all of the major search engine bots don't parse Javascript. For end users, nofollow doesn't mean anything on a link either.
It's best to rel="nofollow" links via PHP or manually.
If you want to use PHP, use preg_replace to add nofollow links. PHP is parsed server-side, so bots will see the nofollow.
At the moment, this plugin provides zero functionality.