Congress certainly could "legislate" waterboarding away under its Article I powers to "make all laws" concerning the armed forces, though this begs two issues:

1. Only part of the Intelligence Community constitutes the armed forces for purposes of Article I jurisdiction, so this would only get at part of the problem; and

2. The administration has already reserved to itself the right to ignore acts of Congress under the presumptive authority granted under Article II's commander-in-chief clause.

My assumption is that the panoply of Bush-era executive privileges will be brought up for strenuous review by the Republican Party in Congress once a Democrat is elected president -- they're not going to be at all happy with the idea of President H. Clinton having Bush/Cheney powers.