Gates’ point regarding the use of force clearly refers to the most (politically) plausible type of attack, some kind of stand-off strike with air power or cruise missiles. Clearly if the US had as a preeminent foreign policy objective the elimination of Iran’s nuclear program and regime change, it is within its capabilities to do so. As you rightly point out, Eric, no president should take the latter option off the table. I wouldn’t play it up, either, since I doubt such a threat would be perceived as credible.
However, what’s missing from Gates’ analysis (and yours, at least in this post, and I’d be curious to hear your opinion) is whether or not delaying the Iranian program for several years is a good idea. Gates seems to think that the timing of Iran acquiring nukes is irrelevant. With changing political forces in the country, I disagree–a difference of three years may be fruitless, but if in three years we’re able to strike again (say, sabotage if they move underground… we’d have years to work on that plan) that could buy us yet another few years. Of course, we’d be taking a perception hit among the Iranian population with each strike, so we’d have to hope that in relative terms the elusive Iranian moderate were to gain more than his hard-line brothers.
This all leaves open the question of how good our intel on the program is. It is nasty to think about, but if we know the scientists in Iran who are working on the program, then I’d suggest it doesn’t matter what’s buried in the desert if no one in Iran capable of using it is still breathing.