He was being charged with the felony of downloading/distributing research done using public funding so that it could be made freely available to the taxpayers who funded it. JSTOR had no interest in prosecuting him, but the US Attorney's Office decided to go ahead anyway.

This would be a perfect opportunity for a White House pardon.

Those are only available to the guilty.

Is that the case in the US? My impression is that Ford gave Nixon a blanket pardon even though Nixon had not (yet, probably) been found guilty of anything.

You are correct: http://www.factcheck.org/2008/06/blanket-pardons/

A promise of a pardon would have done just as well, especially for federal prosecutors. The DOJ isn't going to make a big case out something their boss has promised to throw out. That said, the president being superinvolved in an ongoing case like that would be very strange.

I assume you mean convicted, but Ford gave Nixon one.

Actually I do mean guilty, as I was under the impression that you have to accept your guilt before you could get a pardon.

"Everything bad that happens is because this country sucks, everything good that happens is because our community is awesome".