I work with organic farmers all the time. They always complain about fuel costs cutting into their margin that is supposed to be so much higher. If they are spending more on fuel than the conventional farmers that I work with, they are using more. Just first hand hearsay, but I trust what I hear from them.
Your logic isn't sound. Diesel isn't the only source of carbon in a carbon foot print. It's possible that organic farmers make up the extra diesel based carbon elsewhere. I admit, I don't know if the other offsets put organic ahead of conventional farming or not.