The number one protection is simply that the long lived waste products do not spread easily. The are almost insoluble in water and they tend to cling to every surface they get into contact with. Even if all the containers in a waste repository would fail it would still take a very long time for any long lived waste products to reach the surface and then it would be in extremely low concentrations. Its as close to fool proof as anything can come. Even if someone in the future drill straight down into the repository the exposure to radiation will still be very restricted. The swedish repository is even expected to handle a new ice age.
It was mostly iodine, cesium ect. I doubt much plutonium was spread far from the reactor, it just doesn't spread easily. Nuclear weapons test has spread much much more plutonium into the atmosphere.
IMO the main advantage of getting rid of long lived waste by transmutation is the PR side, then the nuclear industry can say that the waste problem has a solution and its not a problem anymore. The environmental organisations have already made the public sceptical towards geological storage. With carbon taxes that option will hopefully be economicaly competitive.
Seems like most fast reactor projects in the pipeline have the goal to be able to accept fuel with a mixture of Pu and minor actinides like that LWR's produce and that solves that problem without exotic concepts like ADS. But even the economics of ADS might become fairly reasonable. Atleast if it turns out as optimistic as the researchers working on it hopes.
http://www.neutron.kth.se/publications/library/DanielMSc.pdf
One argument that sometimes pop up in sweden is that after some time(tens of thousands of years) has passed most of the plutonium in the repository will be Pu-239 since the other isotopes have shorter half lives. So it could become a "plutonium mine" for future generations. I have a hard time taking that argument seriously since the current generation can not be expected to prevent the conscious descisions of future generations, but arguments like that has to be countered for nuclear to gain trust again. Just another reason to destroy it for good.
The best plan any country has so far is by far India. They plan on three stages.
Stage one, use heavy water moderated reactors running on natural uranium.
stage two, burn the plutonium and minor actinides produced in stage one in fast breeder reactors that breed u-233 from thorium instead of plutonium from u-239.
Stage three, use the u-233 in breeders running on pure thorium fuel cycles.
Stage two takes care of all long lived waste and stage three no longer produce any significant ammounts of long lived waste.
A thorium(u-233 breeder fuel cycle, especialy with molten salt reactors, looks very good next to a Pu breeder fuel cycle if looking at it from a global perspective with the HUGE ammounts of Pu that would be in circulation if nuclear power is to play a significant part of energy production.