Three points in response:
1) Netanyahu may not himself have mentioned Amalek to Goldberg, but Goldberg quoted an aide assuring readers that Netanyahu views Iran as Amalek. He then tied this historically Jewish reflex -- viewing all subsequent enemies as reincarnations of the Biblical bogeys -- to Netanyahu's father's scholarship, the central theme of which he portrayed as the irreducible racial hatred borne against the Jewish people by the perpetrators of the Spanish Inquisition. If readers concluded that Netanyahu views Iran as Amalek, Goldberg bears some responsibility (and credit!) for that.
2) Andrew Sullivan, by emphasizing the damage that the Amalek-Iran equation does to Israel's diplomatic stance rather than what it says about Israeli leadership's unspoken worldview, got the problem backwards (and gave Goldberg the opportunity to focus much of his defense on a red herring - Israel's diplomatic acumen). The whole point of Goldberg's unveiling of the Amalek metaphor is that it gets at the Israeli unconscious.
That's what's so disturbing -- we have the leadership of a powerful modern nation state viewing its enemies in terms of the stylized, moralized victors' history codified in a 2000+ year-old chronicle. Of course Israel is not planning to massacre tens of millions. But atavistic fears underpin Israel's response to current dangers that are alarming enough. And however softened and spiritualized by the rabbis over 2000 years, the Biblical demonization of Israel's enemies remains an important element in Jewish consciousness -- and Israeli action.
3) Goldberg protests:
In any case, this whole debate is a perversion, and not only because genocide is the specialty of other religions, and not Judaism. Iran has called for the elimination of the Jewish state, and seems to be building nuclear weapons that could make that a reality; Israel simply seeks to protect itself from a country that wants to exterminate it. If Israel does strike Iran, it would bomb military targets while trying to minimize civilian casualties. Iran, through its proxies Hezbollah and Hamas, already has a long and distinguished record of murdering Jewish children. There's simply no equivalence here. Yes, Israel does various idiotic and immoral things. But it isn't, even on its worst day, the Islamic Republic of Iran.All true, to a point. Iran has called for the elimination of the Jewish state, though its leaders always carefully avoid suggesting that Iran itself plans to effect that elimination by military means. But Goldberg here reproduces the endless disconnect -- which I think Ezra Klein pointed out -- between Israel's focus on intent and its Muslim neighbors' focus on action. Yes, Israeli action against Iran would focus on military targets. But it's likelier that Israel will make that attack, and kill hundreds or thousands of Iranians in its targeted strike, than that Iran will deploy nuclear weapons or otherwise directly attack Israel. Israel may indeed try to minimize civilian casualties, while Hezbollah and Hamas directly attack civilians. But Israel has killed a lot more civilians in its struggles with Hezbollah and Hamas than those enemies have Israelis. That's a difference in power, not intent. But Israel's neighbors focus on the body count.
One could counter that the number of Iranian civilians killed by the Iranian revolutionary regime probably outstrips the number of civilians that Israeli armed forces have killed in the country's entire history. I agree with Goldberg that there's "no moral equivalence" between Israel and Iran. But an Israeli preemptive attack on Iran would bring equivalence a lot nearer. And the Amalek mindset makes such an attack a lot more likely.