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During season 5, River Song was in jail because she killed a very good man.
In season 6 episode Let's Kill Hitler, we learned that that very good man was The Doctor.
But, in the end of the season 6, we learned that River Song never killed The Doctor. For the justice department, it shouldn't be mystery as The Doctor used Teselecta itself to fake his death.
Why was River Song arrested?
Why was River Song arrested?
Because as far as anyone besides the Doctor, River Song, and the Teselecta crew are concerned, she killed the Doctor. This is the result of faking his death; people think the death was legitimate.
But, in the end of the season 6, we learned that River Song never killed The Doctor. For the justice department, it shouldn't be mystery as The Doctor used Teselecta itself to fake his death.
The Doctor must have sworn the Teselecta crew to silence on the matter. Otherwise, it would have been a pretty terrible faking of a death.
In the original timeline, she was arrested for the murder. But The Doctor changed the timeline somewhere after the murder occurred, thus causing the timeline to change after the point where she had already been arrested.
Changes in the past can alter events that happen in the future and vice versa. In The End of Time, The Toclafane simply vanish when Jack destroys the Paradox machine, But the invasion had already begun. The effect took place after the invasion had already begun, thus causing a mere "update" in the timeline.
In a similar manner, events in the present caused the change to take effect in the future, where River had already been arrested, but all of sudden the man she murdered no longer existed. (Just like the Toclafane simply vanished)
As for the Justice Department & Teselecta, The Teselecta were very specific on not changing the way a person died. According to the timeline prior to The Doctor erasing himself, The Doctor was killed by River Song at Lake Silencio. Which they maintained, and they also got to save the Good Man. There was no reason for them to rat him out to the Justice Department. Also, The Teselcta was destroyed in the events of The Wedding of River Song.
So finally she was pardoned after the events of The Wedding of River Song and before the events of Season 7, The angels take Manhattan this is cleared.
As other said, she had to let herself be arrested and stay in Stormcage to protect the Doctor. She says so in DotM when he asks her to travel with him full time: "I have a promise to live up to. You'll understand, soon enough." The Silence was watching at the beach after all as we saw for ourselves. As for the Teselecta crew, we're never shown they were there with him. He very well could have asked to use it or if they were sworn to secrecy, part of that was leaving the records unchanged that Melody Pond killed the Doctor at Lake Silencio. Captain Carter after all did promise to do whatever he could to help the Doctor. As for her pardon, at the Byzantium she says she will be up for a pardon and HOPES she will get one: "I might have done enough to earn a pardon this time." In Manhattan, she says that at her pardon, they couldn't find records of the Doctor and had to release her. So he didn't rewrite her pardon or time in Stormcage. He just got her another reason to be pardoned.
He actually DOES try to rewrite time once for her: at Lake Silencio. He's going to fake his death and get out of her life because he thinks that's best. (She rightly gives him holy hell about taking the decision away from her. He's actually manipulating her like the Silence is and she is now BURNING. It's why the chess queen metaphor is set up and repeated throughout that episode.) But he's doing that without giving her the screwdriver, his name, or the other things she has for the Library, so he's rewriting her future to hopefully make things better while still trying to preserve what they have. Typical Doctor: do what I say, not as I do. (BTW, if anyone is interested, River saying "do as we're told" is a Classic Who reference. The Fourth Doctor used it as Rule One with Romana and after her. He had a different one for Leela. :) ) So of course River with her knowledge of him would know it. It's just one of the Classic Who and Davies references with River alone.
Although she was arrested for killing the Doctor, we found out at the end of series 6 she didn't actually. Only Amy,Rory and River knew he was not dead.
