I don't think that's what it's saying at all. I think it's supporting the theory that this disease is part autoimmune, part genetic, and part bacterial.
It's still saying our immune system overreacts, and that's the reason for the immunosuppressants. Of course if they could come up with an immunosuppressant that only targets the cells in the intestines that get out of control, we'd be golden ;0)
However, it's still leaving an opening for our immune systems not reacting enough in some cases, and not killing the bacteria.
So in my humble opinion, they're repeating what they've been saying for a long, long time. They've just found some new genes associated with the disease, but are still not sure how they tie in to any of it, and our disease could be bacterial, genetic, and/or autoimmune.