http://abcnews.go.com/GMA/story?id=125593 If you look at the drugs we know he was taking I don't see how a little marijuana could hurt things. Here is a generally accepted list of medications that there is a consensus on.

"The medical records reveal that Kennedy variously took codeine, Demerol and methadone for pain; Ritalin, a stimulant; meprobamate and librium for anxiety; barbiturates for sleep; thyroid hormone; and injections of a blood derivative, gamma globulin, a medicine that combats infections.

During the Bay of Pigs fiasco in 1961, and the Cuban Missile Crisis in October 1962, Kennedy was taking steroids for his Addison's disease, painkillers for his back, anti-spasmodics for his colitis, antibiotics for urinary tract infections, antihistamines for his allergies, and on at least one occasion, an anti-psychotic drug to treat a severe mood change that Jackie Kennedy believed was brought on by the antihistamines."

This comment from the article speaks a little more directly to your point though: "As amazing as the list of drugs Kennedy took is the fact that it was kept mostly secret. To this day, his closest aides don't know or won't admit the extent of his ailments."

Now I'm curious!