Where do we put the waste from industrial society in general? The material flow through the renewable energy system will still be but a fraction of the flow through the economy as a whole. The US makes 100 million tonnes of steel annually, for example. There is no need to use any toxic (or, really, uncommon) elements in renewables, so recycle what it makes sense to recycle and just landfill the rest. This is sustainable indefinitely.
In the very long term, humanity might face a problem with exposure of crustal rocks by mining operations. This causes reducing materials in the rocks to react with atmospheric oxygen, gradually depleting that oxygen. The long term solution to that will be to bury some reduced materials to compensate (the production of those materials released oxygen when oxides or CO2 were reduced). So, some level of sustained burial of waste material is not only acceptable, it's likely to be necessary.