Granted, the conviction rate of the Justice Department is as high as 97%[1], so it's certainly likely. But if you have had any experience with litigation whatsoever you would know that there's nothing at all that's certain in a high profile trial such as this one.
Assuming the jury is allowed to hear most of the relevant facts that have been released to the public, he will be found guilty of (at least) the narcotics conspiracy charges. Could there be a mistrial? Sure - those happen for any number of reasons. But he would still be found guilty at a retrial. The facts won't change. While I am no fan of the FBI (or the harsh prosecution and sentencing of non-violent offenders in general), in this case they appear to have done their job quite well and are going to get their pound of flesh. They methodically built a slam-dunk case - largely with the help of Ross Ulbricht himself.
[1] http://www.justice.gov/sites/default/files/usao/legacy/2013/...