I believe that Snowden should have been treated with more respect by the federal government. He has become something of a folk hero in recent times, and rightly so: Snowden revealed the extent to which the NSA is spying on us. When the government made moves to discredit him, this only made them look more guilty - a low blow indeed.
The disclosure of emails sent by Snowden seeking clarification of the force of law of executive orders was a pretty low blow by the agency. Snowden public disclosed information about the NSA's illegal surveillance program that have since been changed because it was improper in the first place. This makes his actions clearly that of a whistle blower, and ad hominem attacks by the agency to discredit him personally because they don't like his methods seem pretty low.
Edward Snowden did the world a really big service when he exposed the NSA for what they were doing. After 9/11 the US government had the perfect reason to invade our privacy. Under the guise of preventing terrorism from happening the NSA monitored innocent civilians who had not even seen a terrorist outside of the television.
No, the government was justified in any actions it took against an individual such as Edward Snowden. Discrediting such an individual, one guilty of exposing many deeply classified government secrets to foreign powers and enemies, is justified. It is a matter of national security to try to discourage individuals of committing similar acts in the future, and national security is the feds' priority.