We will concede that the DEA is wrong in this case (as I feel they are in the whole War On Drugs).
The ATF's own form 4473 specifies "unlawful use of, or addition to" as the dis-qualifier and a medical marijuana user is neither.
By it's own specifications, the ATF is wrong in this restriction.
As far as the 2A not having been formed when drug use was prevalent, it was not unknown then.
However, the restriction should be not on the use of a substance, but the illegality of it's use as illegal acts makes one a criminal and that is the restriction.
I feel that the intent of the 2A was so honest and honorable men could be armed for all the usual reasons and several of the writings of the Founding Fathers support this.
However this also might not be accurate. I'd not be surprised if the Founding Fathers would require most criminals to go defenseless where they to keep away from the populace in general and survive in the wilderness.