He was working with stolen documents. He saw files he wasn't cleared to see. Of course the government wouldn't clear him. He would have been better off to tell them that he did not want to be exposed to any classified material while working. Once you see what classified information is, you know you can work without it. The disadvantages, such as lifetime censorship, and control, outweigh the advantages of a brief government job.
<He saw files he wasn't cleared to see. Of course the government wouldn't clear him.>
To me, that makes no sense. Clearing him provides the opportunity to debrief him on what he's already seen, make him disclose any contacts requesting that information, and how to properly handle what he remembers (if anything) and what new information he is exposed to.
This is like refusing to give Sullenberger a pilot's certification because he might find water landings fun and make them a habit.
If you "make him disclose any contacts requesting that information," you've waded pretty heavily into the 1st Amendment. Should all journalists be obligated to discuss their past reporting with the government? Should only those journalists whose reporting meets government standards be eligible for a government job? Why not just go all the way and license journalists? Some countries have done so. Then you could take away his license for looking at the Snowden material.
