I don't know about them eating forbidden food, as I've never really tested things like that (I guess I've forbidden food before, but not en masse). What you should do next time you're in a similar situation, is dump a turtle, so it rots and you can use the shell and bones without having to wait for one of your guys to eat it.
That said, if they did touch your forbidden stuff, then maybe you indeed did something wrong. You can mass-forbid things by using a key combination that starts with "d" "b" something (probably "f", but there will be a list of possible options for forbidding, dumping, and so on, so you'll figure it out), so if you do that over all your food stockpiles you can then manually unforbid (aka claim) some turtles or whatever you need them to eat.
Also, if your stonecrafter is your main source of trade goods, then I recommend trying something different. What I always liked to base my exports on was prepared meals. You set up a bunch of farms, more than you think you'll need, use relatively few farmers (I use one, who is able to go from proficient [I give him 5 growing skill points on embark] to legendary after like 1.5 or 2 years of tending 4 farms of 3x5 tiles each; I recommend turning on "only farmers harvest" in the "o" menu) and have a cook make your plants into roasts. Concentrate especially on quarry bushes and sweetpods and process them into bags and barrels, respectively, as they yield large stacks of ingredients for your roasts.