Penalize the site or the story? Should Google keep it out of search until it shows up on the "greater" web or are you advocating punishing the whole site because they have some content exclusively walled for a certain amount of time?
That line of thinking also begs the question whether only freely accessible information should come up on web searches, which would rule out any links to many professional journals which survive by subscription and/or fees per article. If you're punishing Wired for putting articles behind walled garden then it makes sense to punish all walled gardens and Google search becomes a search engine cataloging only free articles.
There is certainly a discussion to be had where major sites are allowing Google to spider paywalled posts such that the content comes up in results based on hidden-to-the-rube words, but that's for another time.