There seems to be a slight confusion in some quarters regarding the grounds on which six Supreme Court justices upheld Oregon's assisted suicide law against the U.S. Attorney General's attempt to make it inoperable. Hammer of Truth assesses it thusly: "In an obvious bout of dementia, the Supreme Court ruled today – despite the obvious fact that FedGov does indeed possess the legal authority to withhold the medical marijuana that may well prevent the terminal condition to begin with — that conditional assisted suicide laws, passed by state governments are beyond the reach of centralized state authority."
The ruling is really more about separation of powers than it is about state sovereignty, and while some may see the decision by the four liberal justices plus O'Connor and Kennedy as "case-by-case" federalism, I am more inclined to view it as the majority's attempt to police the boundaries of executive authority when it seems to reach beyond what Congress granted. I'm fairly sure that if Congress passed an explicit ban on the use of legal pharmaceuticals for suicide, and said that physicians who made such prescriptions no longer would be able to be part of that stream in interstate commerce, the Raich majority would have upheld that statute as constitutional. However, the federal government is not one giant blob of coercion, and it's not at all demented for the Supreme Court to consider an action taken by Ashcroft on his own intitiative to be improper, while viewing one taken under the clear authority of legislation to be permissible.
Thomas's dissent does interestingly challenge the distinction between the Raich decision and that made for Oregon, but on the grounds of the majority's allegedly inconsistent interpretation of the Controlled Substances Act's grant of power to the Attorney General, not so much on state vs. fed kind of federalism. Still, from what I understand, any CSA prosecution involved in the Raich scenario would be against those who engage in the federally prohibited manufacture and distribution of marijuana, whereas Ashcroft sought to go after physicians even for writing prescriptions.