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.
Even though it may be good policy for the Supreme Court to act that way, that's a separate question from whether they in fact do operate in that way.
There is extensive literature (a subset of "legal realism" which accounts strategically for judicial action) which claims that judges do in fact incorporate policy considerations in decision-making. Secondly, it's widely acknowledged that the court frequently and with considerable influence advises Congress to change the law. In that context, it might be fine & useful for this article to speak in policy terms to the Court.
This ignores how the patent statute is written. Congress sets extremely broad principles for what is patentable and leaves it to the courts to work out the details. That process of interpretation inevitably involves making policy judgments.
This isn't unusual. Constitutional concepts like "reasonable search," "cruel and unusual punishment" similarly invite courts to make policy judgments.