Nonetheless, there are two separate and completely orthogonal questions here.
1. Is it good policy to allow software to be patentable, and
2. Does existing law allow for software to be patentable?
I am fairly agnostic on question one, and about three Juris Doctorates short of being able to answer question two, but it's the Supreme Court's job to answer question two without any regard whatsoever to question one.
This article appears to be arguing about question two based on his opinions on question one, which is like arguing that a cat is a handbag because you want to be able to take it as carry-on luggage.