Per your example, Snowden and Manning obtained information about ethically unsavory or illegal activities committed by the government. They brought these issues to the public's attention. Snowden, for example, was able to provide substantial evidence of the mass surveillance apparatus of the NSA that was often dismissed as some conspiracy theory prior. This was civil disobedience.I'm curious what people here who want Hillary indicted think of people like Snowden/Manning who actually, intentionally, and willingly compromised national security since I seem to notice some people that feel that Hillary should be indicted feel like whistleblowers should be pardoned by the government.
Ideally, I do believe Snowden should have had a trial and and the rest, if he stayed (i.e., "Under a government which imprisons any unjustly, the true place for a just man is also a prison." [Thoreau, Resistance to Civil Government]). However, it's not likely Snowden's trial would be, by any means, reasonable, nor his punishment fair, and leaving the United States to seek asylum elsewhere is sacrifice enough. I don't know enough about the specifics of Manning's case, so I have no comments on her situation.
Clinton using a private email server was not a means to bring ethically unsavory or illegal activities committed by the government to the public's attention. She acted as if regulations and standards for government employees were flimsy guidelines and acted in her own authority (which leads to questions about the security of her communications, etc). This was a general case of the rules applying differently based on one's power.
In honesty, your simplification is equivalent to a juvenile comparison of self-defense and murder. In both cases, a person dies, but in one case it's reasonably justifiable, while in the other, it's not. A person being dead isn't how the situation is judged. Similarly, classified information being leaked isn't how the situation is being judged; the reasons behind classified information being leaked is being judged.