So, what you want is a custom workshop with a reaction that requires one worthless stone and has no product?
Here's something off the top of my head:
[BUILDING_WORKSHOP:JUNK_STONE_GRINDER]
[NAME:Junk Stone Grinder]
[NAME_COLOR:7:0:1]
[DIM:3:3]
[WORK_LOCATION:2:2]
[BUILD_LABOR:MASONRY]
[BUILD_KEY:CUSTOM_SHIFT_S]
[BLOCK:1:0:0:0]
[BLOCK:2:0:0:0]
[BLOCK:3:0:0:0]
[TILE:0:1:' ':' ':150]
[TILE:0:2:' ':' ':'/']
[TILE:0:3:'-':' ':' ']
[COLOR:0:1:0:0:0:0:0:0:6:0:0]
[COLOR:0:2:0:0:0:0:0:0:6:0:0]
[COLOR:0:3:6:0:0:0:0:0:0:0:0]
[TILE:1:1:' ':' ':'=']
[TILE:1:2:'-':' ':8]
[TILE:1:3:' ':' ':150]
[COLOR:1:1:0:0:0:0:0:0:6:0:0]
[COLOR:1:2:6:0:0:0:0:0:6:0:0]
[COLOR:1:3:0:0:0:0:0:0:6:0:0]
[TILE:2:1:'-':' ':8]
[TILE:2:2:' ':' ':8]
[TILE:2:3:' ':150:' ']
[COLOR:2:1:6:0:0:0:0:0:6:0:0]
[COLOR:2:2:0:0:0:0:0:0:6:0:0]
[COLOR:2:3:0:0:0:6:0:0:0:0:0]
[TILE:3:1:150:' ':8]
[TILE:3:2:' ':' ':8]
[TILE:3:3:' ':240:' ']
[COLOR:3:1:6:0:0:0:0:0:6:7:0]
[COLOR:3:2:0:0:0:0:0:0:6:7:0]
[COLOR:3:3:0:0:0:7:0:1:0:0:0]
[BUILD_ITEM:1:NONE:NONE:NONE:NONE][BUILDMAT][WORTHLESS_STONE_ONLY][CAN_USE_ARTIFACT]
[REACTION:GRIND_JUNK]
[NAME:grind a worthless stone]
[BUILDING:JUNK_STONE_GRINDER:NONE]
[REAGENT:A:1:NONE:NONE:NONE:NONE][WORTHLESS_STONE_ONLY]
[SKILL:MASONRY]
Not 100% positive it'd work(i've never made a reaction without a product, though i have made reactions that were supposed to have a product and didn't so i can't imagine anything terrible will happen), and it'll look like a soap maker's workshop(because i just copied it and changed the name and labor), but there can't be too much wrong with it. You'll need to go into the entity_default raw file and add [PERMITTED_BUILDING:JUNK_STONE_GRINDER] and [PERMITTED_REACTION:GRIND_JUNK] under the [ENTITY:MOUNTAIN] section.
Also this will(obviously) require the masonry labor, and will give masonry exp to whoever does it. If that's a problem for some reason, you can change "MASONRY" to whatever, like "NONE" or just make up a word, and it'll allow anyone with any labor enabled to use it(You might want to profile it to someone who is otherwise useless if you do that, because your broker or doctors might end up grinding stone instead of trading or working on patients or whatever)
Also, most importantly, even if you add this into the save you're currently playing, it most likely won't be available, it'll require you to generate a new world.