An atheist has no need to defend metaphysical naturalism to criticize the cosmological argument, so that's a red herring. You're trying to drag the critic into Scholastic territory, to bog the critic down with the question-begging principle of sufficient reason. Causal closure can be affirmed on methodological or pragmatic grounds. Methodological naturalism is what's relevant to the scientific approach, not the baldly metaphysical kind.

I've got an article coming out in a week or two that's specifically on the relation between atheism and agnosticism.