I don't know the details of what exactly the supremes did allow them to patent. As I said, if it's the novel lab or field techniques that allow testing for the BRCA1 gene, that may be fair enough. But if it's the complementary DNA sequence itself, that's really no different to patenting the BRCA1 gene (which the supremes disallowed).
An analogy might be a court saying that you aren't allowed a patent on the 23rd page of "Wuthering Heights", but letting you obtain a patent on the same with all occurences of the words "The" and "A" deleted. Complementary DNA is the original DNA with sequences known as introns deleted.