It's a non-issue. On your resumé, and during the interview process, it will just say "MA in CS, Stanford University". Assuming you ever need to "produce your papers", that will be handled by HR, who will not consider the online origin of your degree, so long as it's from the same Stanford they already know and love, to be an issue.
Pretty much your only concern pre-hire is to encounter someone who is very familiar with Stanford, or an alumn themselves… And so long as you're honest about why you don't remember Professor X, Library Y, or Froyo Shop Z, you probably won't be discriminated against because of it…
Still, if you do have opportunities, even post-grad, to become involved with Stanford programs/departments/events/etc, then that will help immensely for the "intangible" that employers do seek out of top-tier grads: the ability to network and recruit more top tier grads into the company.