The ability to engage in charitable discourse is simply a skill that can be taught like any other. Parents could be teaching it to their children, but socially and culturally we haven't yet made it a priority. We should.
True, rationality can be pervasive, and it can be taught, but it can never be totally dominant. Our primitive substrate keeps coming out, and that is every bit as pervasive as rationality.
Someone suggested turning that hierarchy of disagreement into tags that people could assign to comments on a debate site, and filter accordingly. I built something of precisely this sort for my master's project, and believe the idea should be implemented for nearly all online communications. It's doable, and an effective way to impress a great many people with the value of rational discourse, to which they simply may not have had enough exposure to appreciate.
And there is, I think, potentially a tipping point or critical mass where a culture of charitable discourse enters a positive feedback loop and makes gains even faster than before.
Whatever the case, I think there are definitely plausible means for improvement. They deserve to be tested.