Magma dumping takes a season to get rid of the molten rock, like a blood splatter token. Atom smashing is hence slightly preferable, if not quite as dwarfy as using magma as your garbage disposal chute.
Atom smashing also has the advantage of allowing you to sort through the dump site for the things you don't really want dumped beforehand, like if you strip caged seigers naked to loot their goblinite for melting and giant cave spider silk loincloths for decorating with spikes of green glass and selling to elves, who for some odd reason apparently like to wear loincloths made to cover genetalia of creatures smaller than them that are menacing with jagged glass spikes.
The problem is that things like catapults and atom smashers and magma or chasm dumping all take dumping jobs... which by the time you have 10,000 stones lying around is a job that takes years to accomplish. Those are solutions for when you are removing stone as you go along. When you have THAT much stone, sublimating some of the worst offending stones will probably be your best bet, and all I can say is boozecook a little and put your masons under a waterfall for happy thoughts as you vaporize 2/3s of their life's work.
Workshops are fairly easy to rebuild (I mean, really, it's just one stone, and you just said you have 10,000 lying around... compared to 10,000 haul jobs, 40 workshop building jobs is nothing), and if you can avoid a tantrum spiral from sublimating stone, you can just rebuild everything with economic stones or obsidian or the like.
Otherwise... well, I'm actually going to try that catapult, but for now, I have a neat bismuth (for the magenta color) atom smasher with a dump site beneath it.