What I think the article was doing was illustrate (by being absurd) the absurdity of Krugman’s original article by using his own (fractured) logic against him.
Krugman’s position: Incivility on the right led to the atmosphere that facilitated the Arizona shooting; ergo, the right is responsible for the deaths at Gifford’s rally.
And in reply in this article, the corresponding logic is: Krugman is calling for incivility, which according to him leads to politically-motivated mass murder; ergo, Krugman (by his own logic) is a calling for the murder of those he disagrees with (which would be Paul Ryan).
If one has a problem with the lameness of the argument (and one should), it’s a reflection of the lameness of Krugman’s original position.
Now let’s see Krugman argue against himself in defense.