So my limited understanding here and what this case is actually about is that it is not so much trying to prove that Ulbricht had anything to do with the site (because the association was proven), but rather who actually was the mastermind behind the site (and pocketing large sums of cash from transactions). Seems association with such a site would carry a lesser charge than being the one who was profiting off of the marketplace and behind its original conception (this is my limited understanding and it could be wrong).
This story is absolutely insane, it will be interesting to see where this case heads. From what I gather, the bust in the library, screenshots of the chat and admin panel of the site and supposedly a few scrunched up pieces of paper found in the bin of Ulbrichts home are all they have (that we know about). There is nothing that actually proves or disproves that either Ulbricht or Karpeles, are the owners of Silk Road.
Now we just need the defence to come out and claim that Karpeles is actually Satoshi Nakamoto and then we've got ourselves a super interesting case. There is undoubtedly a movie script in here somewhere once the case is finished.