True, you don't really want that stuff to fall into the wrong hands. NASA seem to like RTG's though and used them for New Horizons and a few others. Apparently they share since it's used in Cassini as well.
From my understanding, this shortage is caused by the lack of nuclear power facilities in the USA - which supports the GGP's point about negative political/public reactions to anything nuclear.
The problem is that turning nuclear reactors into Pu238 requires a lot of extra work and equipment. They produce small amounts, but separating it out is tough. You can make more by irradiating other waste products, but that's not easy either. Apparently some stuff used for making nuclear weapons can be used for this purpose (note that nuclear weapons use Pu239, not 238) and the shortage happened because those facilities were closed.
But actively seperating out the required materials is the same processing step as is required for building nuclear weapons, and that's something that's a political problem, and will cost you a lot of money to prove and inspect everything every few days to ensure it's only used for civil uses.