I know they were being abused. I don't want to make them as farmed as the Anomalies once more, but I do think that allowing loot and VP every now and then off them would be acceptable.
So, since they give nothing anymore, would a timer be feasible? They could be added to the existing timer, or something new could be put in place. After all, the people who are doing them for quests, or helping out somebody doing the quests, or just getting credit for the delve... should not be affected by this to the extent of no loot or VP.
Alternatively, make them worth some VP relative to the difficulty... aka maybe 10k.
Whatever you do, please change it in some way to make the stones that drop worth something... as it stands they are just something to throw away.