One thing most people seem to be missing

Rachel did her job as a newspaper journalist. She got a hint of an information from the daughter, unexpectedly. What was she supposed to do? Ignore it? Do you really want journalists to ignore public interest information hidden from the public?
The fact that the daughter is the initial source does not pose any moral dilemma, as it was both unexpected, and non-manipulative. If there is a fault here, it's the CIA mother. Furthermore, she did verify this information. Nobody is crazy to publish something based on what a kid said. In the end the real sources, the ones that made this story happen were the other agents who could no keep their mouths shut at parties.
The prosecutor was an instrument of oppression. The vibe i got was that he was ordered/pressed to act as nasty as possible, meaning that doing his job was not his primary motivation in this case. He isn't the bad guy, but is the guy that lets bad things happen. He even said that he got all he needed. It was probably a message someone higher wanted to send.

Point is this movie is like a manifesto, it takes a scenario in which Rachel is the perfect journalist ( i doubt that journalists are all like that, she's basically a saint), and uses that to show the abuses that can occur when the system places national security above freedom of speech. As Rachel's lawyer puts it, it takes the power from the people, because the government has the tools to shut people up. And then you have a government that is accountable to no one.

Somehow, after seeing the lot of posts here, i think this movie failed. It's a good movie, but it failed on its intentions.

I was rooting for Matt Dillon's character too. I thought he did a brilliant job. Neither could I sympathize with Rachel.
But the point was not the conspiracy. It was the fact that Rachel had classified information which concluded that Erica was the only Agent who said Venezuela had nothing to do with the assassination attempt and the White House knew about it but went ahead with their placement of armed forces in that country. That was something the public had to know. The right to information on what their Government is up to with their armed forces and tax payers funded Ops.