Here's a hypothetical example to illustrate why it's important that secrecy be preserved in cases involving rendition and the CIA in general. I can't use real examples, because, well, the details are secret. Let's say the CIA has a contact inside the government of Yemen. He's proven himself a reliable source over a couple years, and regularly feeds the CIA information. He tells the CIA about a senior official in an Islamic charity based in Yemen. Let's call him Al. Al helps coordinate donations for the charity and travels all over the Middle East and Europe. According to their contact, Al uses his work for the charity to funnel cash to terrorist organizations, and sometimes serves as a courier, delivering sensitive messages between groups.
The CIA considers their Yemen contact to be a reliable source of information, so they grab Al during one of his trips, and transfer him to an Egyptian prison where he is tortured and gives up all sorts of information, some good, and some bad. Overall the CIA is happy because they've neutralized a significant cog in the terrorist financing machine, and maybe gotten some useful intelligence as a bonus. After several years Al is eventually released.
After his release Al files suit in U.S. court, claiming that he was kidnapped and tortured. There's plenty of evidence that he was mistreated (scars, medical condition, whatever), but zero evidence that he was ever guilty of anything. The CIA acted based on information gained through a secret informant who is still in place. He certainly won't be testifying in court, and even revealing his existence could compromise him, and remove a valuable source of intelligence. Their goal was to neutralize Al as a financial conduit for terrorism, and to gain information. The CIA is convinced by what they found, by the interrogations, and by the information given by their source, that AL was who they thought he was. But none of that would appear in court. To the public, and the court system, Al would look like an innocent charity official who was kidnapped and tortured.
I would think it should seem obvious, but secret operations based on secret intelligence need to remain secret. What we see and hear from these terrorist suspects is only the one-sided public face of the situation. It is quite possible that there are numerous cases where the U.S. government acted correctly, but that they cannot reveal why in court, because it would compromise ongoing operations or intelligence sources, or that the evidence against the person is not the type that would be admissible. And again, in case anyone jumps to the wrong conclusions, I am making this argument only with regard to foreign nationals.