One particularly expensive component of stuxnet is deniability. Although the commonly accepted theory for stuxnet's invention is "a state actor", specifically the United States, there's no proof of that at all. And conjecture without proof poses no threat to the US government.

If the government were to, on the otherhand, bomb Iranian nuclear facilities, one small mistake in the plan could ruin their chances of deniability, bringing down international condemnation on the US.