While I agree with you that the real issue here is that software patents should not exist in the first and that this bill actually gives some legitimacy to them (by explicitly naming them), this is still a good thing (IMHO).

Patent trolls basically just throw legal shit against a wall and see what sticks. If nothing sticks it does not cost them anything. This bill would increase the risk to the troll. There is now cost associate with the non-sticky legal shit (so to speak).