Yes, a state's medical marijuana laws put that state in violation of federal drug law, because the federal laws still ban marijuana. A state cannot regulate laws that are different than federal law. Someone who uses marijuana should know that they are still in violation of federal law. A state cannot override that.
Medical marijuana should be allowed in all fifty states in my opinion but unfortunately the federal government still has marijuana listed as a controlled substance. Until the federal government changes their views and opinions on it, it will continue to cause states to violate federal laws when they allow their citizens to use it, regardless if it is for medical use or not.
States have the right to implement laws that go against federal laws, yet citizens do not have the right to break any laws. States who have passed medical marijuana laws and recreational laws leave their citizen out in the open. Since federal law still clearly labels marijuana as a drug, each individual citizen that uses it, is breaking a federal law.
No, a state's medical marijuana laws do not put any state "in violation of" federal drug laws. Being in conflict is not the same thing as violating the laws. Obviously when the feds decide to crack down, there's not a whole lot the state can actually do about it, since federal overrides local, but it's not the same as violating. You can't put a state in prison. Is that semantics? Well, yes. That's what debates are.
Though it may not appear it today, states have rights to conduct themselves in almost any manner they see fit. The federal government doesn't have to resources to stop states from allowing people to use a mostly harmless plant for medicinal or recreational purposes. If these states were truly in violation of federal drug laws, the feds would have come down hard on them by now.
Marijuana laws are an example of states' rights. The federal government allows states to decide the issue. Since all of the states cannot agree on a single law at this time, allowing each state to decide independently is an important compromise. The supreme court has not ruled against states' rights to legalize marijuana.
It seems that as a culture we are always talking about the right of each state to make laws for its people. That is the only way that progress on many issues can be made. So that a state that legitimizes pot for medical reasons is not going against federal law but taking a step to bring it up to date by being on the forefront.