River absolutely did spend time in prison. Every time we saw her breaking into/out of prison occurred somewhere between Wedding and Manhatten.
The reason she was still in prison is explained in a few of the subsequent episodes, though I suspect there's probably some plot holes introduced by the whole Wedding stunt.
River was arrested for the murder of "a great man; the greatest man". Knowing River, I think we all immediately figured out that she was arrested
for murdering The Doctor at Lake Silencio.
We also know that
The Doctor isn't actually going to die during the course of the show,
so clearly she didn't actually do what she was accused of.
The reason she went to prison anyway was to maintain the illusion that her victim was actually dead.
By the time that Wedding happened, The Doctor had realized (through events like Demon's Run, etc.) that he had gotten too "noisy" and made too many people angry. So he decided to go into hiding, and River plays along by taking the fall for murdering him, even though she didn't. Everyone has to think he is dead, so she cannot use his still-being-alive as a defense against his murder.
She stays in prison for that murder for a long time, which she accepts because The Doctor routinely comes along to break her out of prison again.
When we later saw her in Manhatten, she tells The Doctor that she had "been pardoned", meaning she was definitely in prison for something, but wasn't any longer. Note that she doesn't say she has served her time, nor been paroled, meaning somewhere along the line the truth must have come out, but I don't know when/how that happened.
(Note: from her perspective, this puts Manhatten sometime after Flesh and Stone, where she was on "work release", but well before Library, where she was a Professor.)
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