But in reality that's not the prosecutors call to make. In the US laws are challenged in the court system, or overturned by lawmakers. I would say that the current government in the US is not going to be open to changing these things so that requires charges to be brought and a trial to be convened and then let the process move from there.
A presidential pardon solves Snowdens issue, but does not change the law.
It is very much the prosecutor's call to make. Prosecutors aren't (at least in theory) supposed to charge the accused with as many crimes as possible. It is the job of the prosecutor to ensure that justice is served, whatever that might mean given the facts before them. Sometimes that might mean throwing the book at the accused, but in other cases it might mean dropping the case even when it is clear that the accused really did break the law. Unfortunately prosecutors are rewarded for successful convictions, so it is not surprising that prosecutors act as though their job is to charge the accused with as many crimes as possible.
I'd put it a little differently: it's the job of the prosecutor to ensure that public order is upheld. Americans tend to get distracted by the ambiguous notion of "justice" and what is or isn't "just" (even when the two are orthogonal).
Justice is for the courts to decide, not the prosecutor. But whether enforcing a law serves to uphold the public order is up to the prosecutor. And enforcing bullshit laws is just as problematic as being inconsistent in what laws you do enforce.
The laws he broke being immoral/unconstitutional/for the greater good is to be determined by the judge/jury, not the prosecutor.