I don't know if I clearly conveyed what I meant. I mean, by that article, to say that thanks to the females teaming up and punishing males for violence, all bonobos are able to live more peacefully than chimpanzees. (Much like your baboon article.) Using aggression to stop aggression is similar to being "tolerant of everything but intolerance."
Since we are humans, we don't have to use violence; we could do a lot of other things. One better but still imperfect solution is shame, like you said. Imperfect, but certainly preferable to the current state of things.
Anyway, I thought the fact that similar animals so much dumber than us have managed to largely solve their male aggression problem says a lot. And that they did it purely through the females working together, without male help.