No, this is where I think our CIA or NSA needs to step up to the plate and earn their reputations back. It should be a pretty straighforward spy job to gather up all the numbers of these throwaway phones. You now have a short list of phones to agressively monitor, that is, in the form of "record everything". Next those phones need to be randomly dialed at least daily "with an important political announcement" from some candidate the agency has a beef with. Either that or a candidate that wants to cooperate with protecting our nation's safety while getting a free message campaign out of it.
What we've got here is the electronic equivalent of a well-marked animal trail, which any good trapper would recognize as a prime spot for placing a snare. Enemies of freedom want to use throwaway phones? Fine. Let's render them very very very unsafe as possible detonators, and record their lousy planning sessions at the same time.
Let's not go into too much detail.