It's popular to condemn the Supreme Court's decisions if you disagree with them, and it seems equally popular to blame them on the Supreme Court's fundamental misunderstanding of . I'm not saying the SCotUS is flawless—hardly, they are made up of people—but it would behoove authors and readers if you started from the base assumption that you are dealing with brilliant jurists. Indeed, that is how lawyers have to prepare.
The lawyers arguing against the patent were likely aware both of the justices' intelligence and their general interpretations of patent law, therefore chose not to tread the path of invalidating medical patents in general. The questions asked by the justices were fair. Not expressing skepticism does not mean there is no skepticism, for one. We don't find that out until the decisions are written.
Whether this was a case where someone should have gone after medical patents in general is up for debate. In particular, it seems unlikely that the Mayo clinic, which probably has its own medical patents, would try to invalidate the concept itself.
If you read some more of the questions and interactions, you'll see that the Supreme Court seems anything but oblivious: they're trying to probe what should and should not be patentable in a field that involves actions and reactions that are all based in chemical fact. If neither they nor the lawyers can provide a satisfactory test to determine this, then all they can do is decide the specifics of this case.
True change in this area really is something where the Court can only do so much. The definitions of patents in general are determined by Congress and its laws. If we want to change them, we have to focus there. SCotUS has merely become our backup because it's been relatively difficult, particularly in the last 40 years or so, to convince Congress to pass laws that are potentially damaging in any way to the bottom lines of businesses.