In my opinion, #2009 was a configuration issue that should have been addressed in the tracking code, i.e., use piwikTracker.setDomains("*.piwik.org").
(Is this is a result of ?) The user in http://forum.piwik.org/read.php?5,75978 reports that class="piwik_link" no longer forces a link within the site to be treated as an outlink.
One use case would be for stealth redirects.
I agree 2009 should have been wontfix, I'll revert and repackage