This debate has somewhat been overtaken by events in the four-and-a-half years since the article on which you're commenting, but I think your comment still deserves a response.
Firstly, general opposition to nuclear proliferation should indeed be enough to make us "very concerned" about the prospect of Iran, or any country that doesn't currently have one, acquiring a nuclear weapon.
From a certain point of view there is a "logic" to the Iranian ruling class's desire to acquire nuclear arms, just as there's a "logic" to Israel having them (for it too is surrounded by "powerful enemies which would like to attack it"; I'm not sure, by the way, how you arrive at the conclusion that a nuclear-armed Iran would "present far less of a threat" than other nuclear armed nations, unless you think the Iranian state is somehow "more progressive" than Israel or Pakistan). But our job is precisely to "fault" and critique ruling class "logic", including the logic of ruling classes other than "own own".
The idea that "our first concern" in any given instance should be to simply oppose the policy of our own ruling class is merely inverted nationalism. Just because our government says it'd be bad if Iran acquired nuclear weapons doesn't mean we have nothing to say beyond generic opposition to proliferation, or that we have to say, "no, it wouldn't matter", or even "well, it'd be less of a threat than Israel having them" (hey, why not? Let them have one! Bombs for all!).
We're not vulgar economic or geo-political reductionists/determinists. We acknowledge that there is sometimes more that motivates social and political actors than coldly rational calculations of pragmatic "interest". We acknowledge, in other words, the role of ideology.
The political forces currently hegemonic in the Israeli state, for example, are in my view acting well outside of the parameters of "rational" bourgeois politics, even colonial-bourgeois politics. The policies they are pursuing, it seems to me, are straightforwardly bad for the Israeli state from a rational bourgeois point-of-view. They are basing their policies on ideologically-motivated, national-chauvinist expansionism, even where that conflicts with "rational" bourgeois interests. That deserves particular analysis.
Iran, to an even greater extent in my view, is is not simply a rational bourgeois state. It may be moving more in that direction but it is still currently a clerical-fascist theocracy. The role of ideology, of "fanaticism", if you want to use that term, cannot be discounted, even if the US, for its own reasons and in its own way, has also made a superficially similar analysis (although less so recently since their entente).