So, this is a very important case affecting the trend of patent enforcement in a profound way but does nothing to challenge the idea of software or business methods being patentable in a general sense. For anything to change in that regard, Congress must act."
Considering that it wasn't action by Congress that lead to this situation, why is action by Congress required to fix it?
Because 35 USC 101 reads as follows: "Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title."
Business methods are surely processes, and this simple and general language does not admit a lot of ad-hoc, judicially created exceptions like ("but no software patents.")
35 USC 101 read that way long before State Street Bank & Trust v. Signature Financial Group in 1998 got business process patents going. And we have over a century of jurisprudence prior to that on the proper meaning of the word "process" which did not point towards business methods being patentable processes.
Furthermore my understanding is that the Supreme Court has punted on this issue. But since the ruling precedent is from United States Court of Appeals for the Federal Circuit, the window is open for the Supreme Court at some point to disagree with business method patents. (Though Bilski showed no evidence that they are eager to tackle that issue.)
It could always have been read broadly, but was it in practice?
Wikipedia brought up the 1908 Hotel Security Checking Co. v. Lorraine Co and the 1950 Joseph E. Seagram & Sons v. Marzell as examples of cases where courts rejected patents on business methods. Furthermore the USPTO for many years would not accept such patent applications. Not out of capriciousness, but because they really thought that such patents would not pass legal muster.
These stand as examples showing that 35 USC 101 was not always read as broadly as it is being read today.
I read it as, "[Practically speaking,] [f]or anything to change...Congress must act."
You are right that Congress is not the only branch of government that is constitutionally permitted to opine on the scope and subject matter of patents. But, as you note, the Supreme Court has punted on this, which indicates that they prefer to let change come from the electorally responsive branch. Which makes it likely that this decision will be reversed or remanded.
Considering that it wasn't action by Congress that lead to this situation, why is action by Congress required to fix it?