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Why do my comment links look funny? Your plugin is broken.

You probably need to add some css to your theme so that the b.url element is recognized as a link. Please see the instructions under Installation.

Why do my comment links not work? Your plugin is broken.

Your web server is probably not allowing access to the file wp-content/plugins/javascript-nofollow-links/jnl.js. Please see the instructions under Installation.

Is this cloaking, a practice Google frowns upon?

I don't think so. Cloaking refers to serving different content to search engine robots than humans see. This plugin serves exactly the same content to all visitors.

I'm still worried about Google getting mad.

I am sorry to hear that.