1) He clearly and obviously was motivated by desire to enforce what he considered to be the Constition of the US. He may (or may not) have been wrong, but there was no attempt to gain money or intentionally undermining of our country (he could have simply sent the files to Russia or China without publicizing them)
2) He had previously attempted to go through channels and this failed to do anything. But once it went public, real changes were made as a direct result of his actions.
3) There are multiple bad consequences for him remaining outside the US - it's a stain on our reputation and question him and find out any thing more about what happened and what he did.
4) The current situation ENCOURAGES more people to follow in his footsteps, particularly those that desire money or fame. He escaped to Russia, became a celebrity and they made a movie out of his life. That's the ultimate "win" for anyone considering copying him. By pardoning him (and yes, the President is legally allowed to pardon someone before they have been convicted of a crime - we did it before, after the Civil War), we are actually discouraging copy-cats by taking him out of the public eye, reducing his fame.