Yeah its a touchy subject. Although as acysb87 points out, there is absolutely zero room at an airline for staff not adhering to official policies, the whole idea that someone's legally authorized, non-dangerously combustible, prescription medication would be prohibited for transportation (not even consumption) on an airline is highly problematic.

We obviously don't have both sides of the story (perhaps he may have intimated to staff that he might have a "right" to smoke or consume the prescription on-board), but bureaucratic intransigence seems to reign supreme here. IMHO, the guy should've just kept his mouth shut, put it in his carry-on instead of drawing attention to his prescription, and I bet he would've travelled without incident.