Ask yourself this question: What requirement did the scout fail to complete?
2: As a Life Scout, demonstrate Scout Spirit by living the Scout Oath and Scout Law. Tell how you have done your duty to God, how you have lived the Scout Oath and Scout Law in your everyday life, and how your understanding of the Scout Oath and Scout Law will guide your life in the future. List on your Eagle Scout Rank Application the names of individuals who know you personally and would be willing to provide a recommendation on your behalf, including parents/guardians, religious (if not affiliated with an organized religion, then the parent or guardian provides this reference), educational, employer (if employed), and two other references.
I like to look at it his way, many of the scouts we have don't live the scout oath and law 24/7/365, and neither do us adults. The requirement doesn't say that you must never not demonstrate scout spirt by violating a point of the scout oath and scout law.
6: While a Life Scout, participate in a Scoutmaster conference.
I suppose you could just refuse to do a scoutmaster conference, if you think that is the right thing to do. I don't think I would ever deny a scout a scoutmaster conference if I were a scoutmaster.
I always turn back to what the requirements say, not what I think. I think drug use is a terrible decision and is very destructive to one's self and the community at large. Now, there are those that disagree with me that a little weed or a little coke never hurt anybody, and, there might be some truth to that statement, but pretty much everyone with a drug addiction problem starts with a little of this and a little of that.
One of these days, I will be a scoutmaster, and I hope I never have to deal with this situation.
The bottom line is if you don't sign it, an appeal will most likely be accepted if he has done all of the merit badges and can show some documentation on his project.