Let's take the funny example of Amzon vs B&N on the one-click system. Do you think Amazon would not use the one click system if it were unpatenable? In the case of modern software patents, keeping it a secret is equivalent to not using it all. Since you invented it in the first place, I find this outcome to be excessively unlikely.
You are also suffering under the misconception that a lone programmer or programming pair would be incapable of standing up to big markets with a software invention. If his invention is really worth it's muster, he can come out with a profitable product that blows big companies out of the water. I've seen it happen before.