The certificates they sent had a paragraph disclaimer at the end pointing out that the certificate had nothing at all to do with Stanford. This was the only mention of Stanford. This clause was only added because Stanford legal requested it since the classes were taught by the Stanford professors who set up the system, of their own initiative and definitely not something initiated from the bureaucratic side of the institution. Your post suggests that the certificates indicated they were granted or approved or validated in some way by Stanford. This is not the case at all, it is the opposite. I recommend you track down one of these certificates and examine it to your satisfaction.
As far as Coursera, it didn't exist in Fall. It was created in response to Stanford lawyers and bureaucrats going apeshit and shutting the venture down once they saw what a threat it was since the classes were as good as what they were charging for. This caused several of their best professors to resign and leave Stanford.
Stanford is about their reputation, which comes from their top notch professors. With professors leaving, the reputation is worth less than before.
Stanford intentionally isolated themselves from this venture and tried to punish those who pursued it. This shows how committed their administration and legal staff are to the future of education. Not at all, in direct conflict to their most progressive and talented professors.
The future clearly belongs the rogues who are leaving the inefficient and ineffective old system behind to join the ground level grass roots work of modernizing education. This is something that institutions are showing themselves incapable of doing, and it scares them. They won't go down easily. They will fight this, attack the new paradigms, and try their damnedest to retain an economy based on buggy whips that supports their institutional power, wealth and obsolete practices. Many on the forefront such as Salman Khan do not have any teaching credentials or background, and that is how it must be for the old practices do not work.