I disagree. Penny should not be charged with a crime because in a just society he did not commit a crime. He was carrying out the act of a good Samaritan. It's unfortunate that Neely died as a result of Penny's actions but Neely's death was a direct result of his threatening actions.
In a society that bends over backwards to protect the rights of criminals, and I believe it is correct to do so, there is a need for the occasional acts of citizen Samaritans who intercede to protect those unable to protect themselves. This is one such case.
BTW and IMO this is relevant Neely did present a clear and present danger to Penny and all the others on that subway care:
Neely was wanted for punching a 67 lady in the face and sending her to the hospital. Chew on that for a moment.