It's not so very difficult to understand: this is the parallel that Chomsky himself drew, and I believe he did so to insinuate that even a limited employment of force by the US to weaken bin Laden would (as in Sudan) cause more damage in the future than it could possibly prevent.
Frankly, I'm a bit more puzzled by the inability of others to recognize that not all interventions are equally horrible. Special forces operations to destroy bin Laden's networks may be ultimately counterproductive (although that's far from certain), but they're unlikely to inflict many civilian casualties. Even an effort to oust the Taliban needn't be a war against the people of Afghanistan, for they and not the US are the party that has incurred the most suffering at the hands of that wretched regime. On the other hand, we ought to worry about the prospect of a war against multiple states akin to the one Wolfowitz and others have called for.
A query for those who advocate bringing bin Laden and co to trial (as I would if I thought it possible): who's going to bring him into the UN's custody? Do you think that he'll willingly turn himself in?
-- Luke