Not arguing but, fyi: the patent was not on the process of creating cDNA, it was on the product -- they patented the cDNA itself, not the process for creating it. It is a composition of matter patent.
But the information in the cDNA already exists in the mRNA. The justices seemed to argue that removing the introns was the step that makes cDNA patentable, but the introns are already removed from an mRNA molecule that is about to be translated into a protein.