The Supreme Court ruled on this a few years ago. They said that Congress can regulate home-grown marijuana (even though they are only constitutionally allowed to regulate interstate commerce) because the presence of homegrown marijuana affects supply/demand in the interstate market for it:
It seems obvious to me that the authors of the interstate commerce clause didn't intend it to grant the authority to regulate anything and everything just because an interstate market for it exists, but the courts are generally quite hesitant to invalidate Federal laws.
Practically speaking, most drug enforcement happens at the state level. This means that individual users and small sellers in states that legalized marijuana probably won't have many issues, but you won't see ABC Liquor and Cannabis opening its doors any time soon.
http://en.wikipedia.org/wiki/Gonzales_v._Raich
Baffling logic, but I wouldn't be optimistic for the federal authorities to be too foregiving here.