I think we should all look at the example of Mohammad Ali's appeals to the Supreme Court regarding charges of dodging the draft. In a documentary about Ali, I recall the one of the supreme court justice's clerks going back through the record, and it turned out the Ali's beliefs (being a member of the Nation of Islam) did qualify him as a conscious objector much like the Seventh Day Adventists. Before this point the courts has ruled the N.o.I. didn't deserve the same treatment for its members. Ruling for Ali posed a large problem for the Supreme Court, if they ruled in a way that set a large precedent that many people could claim they were objectors the country would have huge problems feeding the established "war machine" (the draft). So the justices went back through the record and found a technicality, as such they found a way Ali wouldn't be found guilty of dodging the draft due to a procedural error. See
http://en.wikipedia.org/wiki/Clay_v._United_States for all the details.
I expect if the court comes to review the facts in this matter they will either be impeded in succeeding due to national security concerns or find a way to decide for the plaintiffs in the smallest possible way to not upset the established order. Very rarely are judicial decisions groundbreaking in precedent. They are more like the tree trimmers of legislation and executive privilege, they typically only trim branches not cut down entire trunks as this ruling would possibly do for Internet surveillance.
So this the world we live in, encrypt your life.