Lets look at Dolomite Lime - an important and often necessary agricultural soil supplement in places that the soil pH is overly acidic. Dolomite Lime is on the USDA Organic approved formulary list and is often labeled as organic by manufacturers. For example:
Pro-Pell-It!® Organic Dolomite Lime.
Unless the product is labeled "Raw Dolomitic Lime" then what you are getting has been processed to increase the purity to agricultural standards -- something that most people don't object to. Another reason for purifying the raw material is that fertilizer labeling laws and the USDA Organic program require the percentage of ingredients to be listed, so rather than make a different label for every bag the raw material is cleaned.
The cleaning process involves a little bit of high school chemistry. The raw material is dissolved in a light acid, and the unwanted material is forced to precipitate out. Then the dissolved
CaMg(CO3)2 is dehydrated into a granular form. It's all good clean fun!
So why is this (and many other) chemical permitted in the USDA Organic Program? Because it meets the letter of the law: when applied according to directions on the label it does not significantly effect local soil environments.
If you are interested in where fertilizer companies obtain the materials they package, check out this trade journal:
Chemical Week