Note that the medical operations have dealt with a handful of nasty busts under Holder/Obama, but don't seem to be closing up shop or going underground. Drive down the right streets in Denver, and you'll pass literally a dozen legal pot shops operating in the open, neon signs and all.
Why aren't federal drug laws don't change because many of the other states won't let them. A lot of southern states are not so open about drugs. This isn't the federal government vs. a few states, its more like many states against many states; there is just a general disagreement in our culture like there was/is about gay marriage.