First, for purposes of this article (and only this article), I am going to make a false assumption.
We will presume that the NSA's actions are entirely legal, appropriate and in no way an invasion of privacy or an abridgement of American rights. Edward Snowden has clearly committed a crime of treason and by all rights should go to prison.
Now, given that 'fact', I still say President Obama should pardon Edward Snowden, with certain conditions (specifically he must return to the US to answer questions in front of a closed session of congress and no longer talk tot he press about anything that happened prior to his pardon, and agree to never again reveal any information whatsoever about his work for the US government).
Why should we do this?
First, given the situation with Julian Assange, we already know the likely outcome for Snowden. Most likely he will remain outside of US clutches, in the worst case locked up in an embassy of a foreign country. If we offer a pardon, we can at least avoid the embarrassment of having another Assange case out there. Ending bad publicity is itself worth it.
Second, obtaining him will not end the issue, it will instead make it worse. If we get him back it will look like we are holding a political prisoner, even if (as we presumed in this article) he is a traitor to this country and deserves no less than life in prison.
Third, capturing him will in not way discourage others from following in his footsteps. Instead it will do the opposite. Look, this is no man selling secrets to obtain a better life. He had a better life and gave it up for principle. He (and many others in this country) considers himself a patriot willing to give a six-figure job, a model girlfriend, and a home in Hawaii, all to fight the nasty evil dictatorship. It doesn't matter that he is wrong and the US is a benevolent democracy. He (and those that agree with him) considers himself to be Nathan Hale. He regrets that he has but one life of pleasure to give up for his country.
You do not discourage heroes by imprisoning them. That ENCOURAGES them to fight on. The people that think we need to discourage copy cats are right - but trying to put Snowden in prison will not in any way discourage them.
Fourth, the way you convince honest, honorable men to lay down arms is to offer them trust and forgiveness, not jail. It discourages others by making them look stupid, not heroic. What, the hero is bravely standing up to fight against the injustice of being told he is pardoned and can go on his way????
Fifth, it would stand as a beacon to other countries showing them the fair, democratic way to handle dissent. By pursuing Snowden we give China, Iran, and other countries moral standing. See, the US is no better than they are, we have our own 'political prisoners'. By pardoning Snowden, we show them that a truely powerful country can handle a bit of dissent - as opposed to dissenters as criminals, we forgive and forget.
Sixth, we get control of the situation back. He will have to agree to certain conditions, we get to question him and we can stop further leaks of information other countries may want.
I see little if any upside from pursuing a criminal case against Snowden. I see huge international political capital to be generated if we pardon him.