Why didn't the Task Force capture Misa Amane? After the final meeting and Light's death, everyone in the room knew the truth. They knew that the 13 day rule was fake, and the rule about destroying the Death Note was fake, too. 

They also had many evidences against Misa (the tapes, fingerprints, hair, etc.), and Light also screamed "Misa write their names".

At this point, they had enough proof that Misa was Second Kira, but why didn't they capture her? Why did they let her go?
I think we need to consider all the times she was held under watch for one reason or another. First was under suspicion for being the second kira, during which she lost her memories and the bulk of the task force then believed she was innocent and harmless (aside from L who was figuring out why she went from determinedly silent to the ditzy blonde) Then after L's death, Near manages to bring up Aizawa ' s doubts involving Light, and even misa. So with Ide and Mogi to back him up, they have Mogi keep an eye on her under the guise of police protection where she does nothing even hinting at ulterior motives (having already submitted ownership to Mikami per Light's order)

Finally you have Near and the SPK keeping her and Mogi in captivity under surveillance again until 1 hour before the meet up where Misa is dropped off at a high class hotel and allowed to call Light.
Near knew full well in his theorizing that Misa was the 2nd kira. But by this point it would stand to reason that they all deemed her no longer a threat. With the last 2 books burned and no sympathetic shinigami to give her a new one and restore her memories, she could really do nothing about the situation and doesn't even know she committed any crime.