How about some sort of destructive system then? A plasma fueled compactor or incinerator could have some kind of use in getting rid of highly radioactive uranium cream cakes.
Or even better, a transformative device to turn the waste into depleted uranium pellets so you can use them in weaponry. Probably not the best idea to turn a normal pistol into an ultra-penetrating cannon in an underwater facility (read : for ss13 this is always the best idea)
Right now I've made three kinds of rods that can be put into the holders.
Uranium is the standard one,
Plutonium rods generate more energy but make an even more dangerous waste.
Plasma rods generate slightly less energy than Uranium, but hardly anything gets wasted.
For uranium/plutonium waste disposal, I'm thinking that engineers would be have many options, dumping them into the ocean by shooting them out a mass driver (While contaminating parts of the map), burying them (the safest option but you'll need a diving suit) or recycling the waste.