The conflict between federal and state law on the matter is ripe for a lawsuit, but there hasn't been much headway on this yet.
There is the Sup. Ct. decision in Raich. I don't find the majority decision compelling, but it does hold in favor of a federal power to make illicit use that in not interstate or commercial.
As a social matter, I oppose MJ use, but as a legal matter I think an individual could plausibly argue in good faith by extension of existing law that his non-commercial use within his own state would allow him to answer "no" to that question.
The problem I see with getting a prescription is that I envision that rx being filled by someone for money. That's commerce.