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.