I also think that specific flags would help, i.e. flag a comment that is against some guideline, with reference to the rule it broke.
One of the worst fallacies, us probably the kind that removed the civility from a discussion, and hence the good faith.
As a side note, the worst kinds of guideline is an ambiguous one, that leaves a lot to interpretation, e.g "act civil" is itself a nice rule, but otherwise useless, better off as a heading above specific clarifications.
HN doesn't need to be Wikipedia wrt comment rules, but a few Wikipedia style rules might be good.