I think people should only be held responsible for their actions if it's for their own good or the good of other people around them. A parent should impose consequences on their children's actions to teach them to behave well. Society punishes criminals to discourage crime. I think society should lock up criminals if they're likely to harm others. That makes sense. But I don't think people ever "deserve" punishment or pain, unless it's necessary for a good purpose. That's why I prefer treatment to punishment, both on a government-policy level and in my personal interactions. I'd rather try to change someone's bad behavior than punish them for it.
And that's why naturalists ought to be so non-judgmental. People may be irrational, be bad drivers, or harm themselves or others, but hey, why should I expect anything more from a species of somewhat-intelligent apes? When I can help someone improve their behavior in some way, for example by helping them better understand the consequences of their actions on themselves or others, by all means, I'd like to do it. But if I'm not in a position to influence someone else's behavior, maybe the best thing to do is just lower my expectations, and remind myself of why that person is behaving badly to begin with. Because of his genetics, his environment, and because he's a close cousin of the chimpanzees, just like all of us.