Well, the W3C didn’t say that opening links in a new window is wrong, they said it was presentational rather than semantic. XHTML is intended to mark up semantics, while CSS and Javascript handle presentation. Using a rel value that isn’t defined in the rec without specifying a profile is technically wrong, but what Javascript and a browser conspire to do with the semantics of an XHTML page is completely out of XHTML’s scope.
And then there’s the other side of the coin, the one that involves actual people with actual problems. WP makes it possible to have comments in popups by deleting two characters in one file, but keeping those popups from being a miserable pain for the average user requires that the site owner find a link to an article that explains how to add some Javascript. Given that WP includes the template for the popup, I don’t see why it shouldn’t also include the Javascript to make it tolerable.