Edit: This is even true if the government ends up agreeing with them about object-level issues (e.g. if the courts agree that something they revealed was illegal or the executive or legislature agrees to change policy).
I'd say that really this just shows the limitations of the concept of whistleblower laws- essentially they're just a feel good concept that lets people blow the whistle against entities the people in power want them too (like the silly Facebook thing).
I don't really have an opinion about Snowden, but I'd say good or bad, if you're really planning on exposing "the system" you can't really expect any protection, and I think it's impossible to build in that kind of protection.
An simple and maybe flawed example would be vigilante justice. Someone can decide to kill someone extra judicially. They may be "right" in some way, but there is never going to be an allowance for it.
The existing whistleblower laws handle cases where a small number of people are, in fact, not following the official rules. This might be sexual harassment or embezzlement or something, or someone otherwise using government resources for personal aggrandizement. They don't really handle cases where a government entity has deliberately chosen (more or less following proper procedures or more or with the acquiescence or support of its leadership) to do something that some people think is bad. What someone might (perhaps dismissively) term a political objection to the entity's decisions or actions.
As for what would have changed, what changed given he publicly disclosed instead? As far as I know, none of the programs he blew a whistle on were ever found to be illegal, no one in charge of them was fired or went to prison, and the major effects have been crackdowns in the way insider threats are mitigated, the depth that clearance investigations and polygraphs go into, the public has become less trusting of the federal government, and backers of authoritarian foreign regimes have a lot more ammunition to paint the USA as full of hypocrites if we ever take any effort to aid resistance to them.
These notions are famously very narrow. A category that doesn't exist in the government's conception is something like "I think there should be a political debate about, or judicial review judging the legality of, this thing which has previously not been subject to political debate or judicial review because of its secrecy". Or "I think this thing is immoral, but it's not necessarily illegal".
It's easy to support whistleblowing on these grounds (especially if you personally agree with those judgments on the whistleblowers' part!), but it's not easy to integrate such exceptions into the official government secrecy system, not least because of their subjectivity.
There are various ideas for official mechanisms that would build in more official adversarial review or high-level transparency for classified government actions and programs. I remember it briefly seemed like Congress might have been willing to create the official FISA court advocate who would argue before the FISA court against the government's legal interpretations and argue that they should not be allowed to use new surveillance methods under prior legal authorities.
Edit (in order to reply to David - I am somehow blocked from replying to him):
I'm not the government. I don't have the legal right to start a war, or to sentence a person to death. If you don't like what I have to say, you can just ignore me. But you can't do that with a government that keeps secrets. Official secrecy robs you of the knowledge required to participate in democracy.
These people have rights too.
And in foreign relations, it's best to remember the words of PM Henry Palmerstone in the British Parliament, 1848:
“We have no eternal allies, and we have no perpetual enemies. Our interests are eternal and perpetual, and those interests it is our duty to follow.
Does your house get searched daily because a child is missing somewhere?
I bet that approach would save more lives than collecting internet data.
And the british aren't the best advisor for foreign relationships
At the end of the day, I'm okay with surveilling others. I don't think it's morally wrong other countries do it to us (barring agreements otherwise).
I have a problem when we do it to ourselves.
Hayao Miyazaki.
Why? US people kill more US people than any other nation. Seems more logical to keep yourselves under constant surveillance. Tight GPS tracking surely will help solving homicides.