"Checks and balances" isn't synonymous with "one branch of government isn't doing what I want, so a different branch of government should do it." It isn't SCOTUS's job to legislate from the bench, even if the outcome would be a net win for society. Checks and balances only comes into play here if Congress has passed a clearly unconstitutional law. In this situation that is very difficult because it has to be proven that software patents are hindering the progress of science. Perhaps that seems self evident to us techies, but a lawyer has to walk into the Supreme Court and prove it to the tune of 5 Justices. I'd rather Congress just pass a law.