I have not really read up on this case, but since it is so high profile, I cannot imagine a judge allowing the case to be thrown out. I think he faces trial any way you look at it. It is really a shame, but they are definitely making an example out of him so that people are afraid to do the same thing...
Even if the judge does not throw out the case, Ross's legal team can appeal any ruling that the Judge makes. If the appellate court rules against him then he can appeal to the Supreme court. I would not at all be surprised if the NSA was somehow involved in finding the Silk Road servers in Iceland and the government may not want to disclose this, if this is the case it would not be all that unlikely that Ross's charges are dropped or significantly reduced.
They obviously obtained the server location illegally, and are going to do whatever they can to avoid revealing that. Maybe they will just never reveal how they did it and take their chances that the judge doesn't throw it out. In that case, it goes to the jury, and I don't see how any jury would find him guilty beyond a reasonable doubt without all the evidence. Only time will tell!
Regardless what you think of Ross (personally, I think he's a fricken Hero!) if he gets found guilty on all charges, it will be a serious blow to certain internet freedoms as we know it!