I know where this sort of argument comes from. but imo Bilski are more relevant to some really odd ball mental process related patents rather than software. Take a look at Bilski itself you will know what I mean. there are many scholars trying to make a huge fuss on this issue. I think that is because you don't get that many new decision on patents so it is a big deal for them. but in reality, i am not sure the impact will be that significant.
so don't start hyper-ventilating yet. talk to a patent attorney, and ask what they think.