Professor Vince Gaffney, when talking about the pits, said that they investigated the cursus and found "two very large pits, one in the east end and one in the west end of the cursus." He reiterates "these pits were inside the cursus." Furthermore, if you stand at the Heelstone on Midsummers Day, then the sun rises over the eastern pit and sets over the western pit.
I am wondering, have you taken your information from the aerial view accompanying your news link? The "New Discovery" on that image must be the "new mini-henge" which this team claimed to have discovered some time ago.
Here's Vince Gaffney's podcast:
http://www.birmingham.ac.uk/Audio/news/Vince-Gaffney-podflash.mp3
He hates the media attention, as most academics do. The "lets get media headlines" is a red herring. However, he was accused of publishing too early. This is a common occuranance at the moment as academics try to get papers published ahead of the REF and published before others discover.
I'm not saying I understood everything he said, but his theory is convincing. (And, as he said, everyone has a right to an opinion and to disagree). Vince Gaffney has nearly 30 years of working in and around Stonhenge. Maybe he has become too close perhaps. Thanks for the opinions here, but I'll stick to science and the professionals.