SG-1 & the SGC almost certainly didn't have anything at all to do with the main Bad Thing (i.e., whatever got John killed), you're right. But if I was following the story right, it seemed as though there was this bureaucratic brouhaha that lead to other big problems on Atlantis (leading to Rodney telling Atlantis not to respond anymore). Knowing SG-1 and Generals O'Neill and Hammond, even if they did nothing to cause the problems, I have trouble with the notion that they did nothing to try to help stop whatever it was. I think mainly it's a matter in the story of distance from SG-1 and the SGC, and not really feeling like the story is actually set in the same universe with SG-1. It just didn't feel right to me. Rodney felt right to me, but the background situation felt less so, if that makes sense.