I tried working on a stone-using civ as well. I ended up with a workshop converting certain stones to bars while using wood as a fuel, then a craftdwarf job, with the stone bars counted as an alloy, and only that civ got to use that "alloy". It took a lot of typing. If you can find an easier way, please tell me.
I know there's a way. I've seen criminals packing stone and gem weapons in masterwork (rather bizarrely made from bituminous coal and some kind of opal.)
Plus you can use custom reactions to make stone weapons take the stone material. Isn't great, but it's a cheap means to make sure everyone's armed. What I'm hoping to do is mod in flint and make both it and chert a ubiquitous stone and the hunters specifically only have access to stone for making weapons. The rest I'm willing to bite the bullet on them coming with only metal weapons, though your work around sounds like it'd be an effective way to make nonplayer invader civs have a pseudo-stone for thier weaponry.
My personal route's going to be having most only have access to their low-use breakable shovels unless they want to buy an expensive copper, bronze, or iron pick from the militants, and use a "dirt sifter" shop to procure flint, obsidian, and chert, copper and tin ores, and gems for the most part, with the first three being the basis of most militias.