As with just about everything else...
It's all about the money.
Let's take a look back at the end of the cold war. National Security interests lost the spotlight, and the DOE started scaling back operations. This resulted in a massive reduction in force(loss of high paying jobs), and considerable impact on local and state economies throughout the country.
Independent states start to take a "what's in it for me" approach to dealing with the federal government. The governor of Nevada(a state hit hard by loss of employment at the Nevada Test Site), tries to block completion of the Yucca Mountain Repository unless the DOE awards contracts for future missions/facilities/jobs to his state.
This is exactly the same scenario that is taking place in SC. The Savannah River Site, one of the biggest complexes in the DOE, has also felt the pinch. The governor of SC is just trying to get something in return for his states acceptance of the plutonium. He has stated that he will block shipments unless he has written contracts in place with the DOE that would guarantee the disposition of the plutonium. Translated, he wants guaranteed construction of new facilities that would stabilize employment and provide state and local revenue.
I just hope this trump card get's him a winning hand and the DOE doesn't just decide to fold.