The fact that no one called in the police has absolutely nothing to do with Penny's situation. I understand that there are people who feel like that in your argument - they wouldn't get involved in any event.
Fine so far. Anyone afraid of the fallout of calling the cops isn't going to get involved.
Mr Penny was charged with negligent criminal homicide for harming anyone. He was charged because his actions caused the death of Mr. Neely. Stopping a rape does not necessarily require killing or even harming the rapist. I find your argument to be ridiculous fear mongering.
But here you are wrong. You seem to have some notion that people can magically be restrained without harming them. That's not how it works--in a one-on-one situation without a big force superiority you can't do it. Look at how the cops handle it--pile on. Because that's what works. They don't have ways to control a person without harming them in a one-on-one type situation, you're holding civilians to a higher standard.