I don't think creating more output than can be consumed is a problem. I think the exponential growth is the problem.
You can produce more iron and stone than you use, too. But when you're mining, you improve your yield through perks and mods, and then you top out and are constrained by external factors, like the irregular placement of ore blocks. In contrast, farming you can do where you want, and your farm can grow from 1 to 2, 4, 8, 16,... plants each cycle (faster with more perks, but still expoential). Your yield never tops out, at least until you're hitting how many times you can swing your fist in a day. A 'progressive tax' mechanic, for lack of a better analogy, would be needed to keep the yield in check, where higher yields incur proportionally higher risks. Spoilage, hungry animals, and I'm sure other ideas could accomplish that.