Currently it's a gray area whether or not employers would have to allow medical marijuana on a employment drug test.
On one hand the Americans with Disabiltites Act (ADA) would seem to provide a huge amount of protection for this. In fact when I worked in H/R any drug a applicant has a prescription for must be listed before the drug test. If he/she tested positive for that drug and they listed it and could prove they had a prescription for it, we had to accept it.
But here comes the gray area. So one would assume the ADA would cover medical marijuana right?
State courts have ruled differently and right now we have over 15 different rulings involving medical marijuana and employment laws. The one thing the rulings have in common is that an employer doesn't HAVE to accept a positve marijuana result. The reasoning being that it's impossible to know if it was the medical marijuna or recreational use.
So as long as the employer makes "reasonable accommodation" they must accept medical marijuana under the ADA.
But you have weird outcomes, for instance, Arizona state laws says an employer must accommodate the use of medical marijuna in the work place, like any other drug, such as injecting insulin. Maine on the other hand prohibits all marijuna use at the workplace.
Of course like any drug, if it could potentially be dangerous, like driving a vehicle, you could be denied for any drug
So it's gonna get very murky and litigious in the future, but remember a lot of companies don't even test for marijuna. The last two places I worked in H/R we "let" people believe we tested for it, but we didn't.