The specific instruction was published on page 18 of the Portland Oregon Mission Resource Handbook, under the heading “missionary helps”, and is replicated below:
“The fact that Oregon state law allows doctors to prescribe the smoking of marijuana for 'medicinal' purposes does not change the fact that marijuana remains an illegal drug according to the federal laws of the United States, and the Supreme Court of the United States specifically ruled in 2005 that federal law take precedence over state legislation in this matter. Therefore, the Church Handbook statement quoted above ('members should not use any substance that contains illegal drugs') applies in this situation. Unless we receive different instructions from the Brethren, no individual who smokes marijuana for 'medicinal purposes' can be baptized a member of the Church in this mission. The prescription drug Marinol (synthetic THC), a capsule approved by the U.S. Food and Drug Administration, provides legal relief to those who take it. Its use under competent medical supervision is not a violation of the Word of Wisdom and therefore does not prevent a person from being baptized.”
It appears the driving issue is legality. Although many local and state laws permit medical marijuana use and distribution, federal law forbids it. Federal law takes precedence over any lesser laws, and the Twelfth Article of Faith states "We believe in being subject to kings, presidents, rulers, and magistrates, in obeying, honoring, and sustaining the law". Consequently, the mission president's ruling correlates directly with the Twelfth Article of Faith.
Note that the mission president uses the specific language "in this mission". This means that while the mission president is speaking for the Church, he's only applying it within the geographical confines of his stewardship. And why do I assume he's speaking for the Church? Because mission presidents, like stake presidents, are the lowest level in the Priesthood chain of command entitled to initiate direct communication with General Authorities, to include members of the Quorum of the Twelve. Consequently, I do not believe this mission president issued this guidance without first clearing it with the senior leadership of the LDS Church.
Unaddressed in the mission president's guidance is the impact upon current LDS members. How does an LDS member who uses medical marijuana answer the Word of Wisdom question during a temple worthiness interview? Base upon the guidance given above, I don't see how such a person could answer Yes when asked if he or she obeys the Word of Wisdom. This not only can lead to denial of a temple recommend, but I foresee an excessively overzealous bishop actually initiating a disciplinary council to try such a member for his membership. While the latter may be most unlikely, it is possible. A discussion on LDS.net indicates there is still some variance on how different bishops interpret and apply the guidance.
Consequently, it is imperative to disseminate this information as widely as possible to prevent any unnecessary and unpleasant surprises. In particular, missionaries have a duty to communicate this information to investigators in advance.
Now whether or not medical marijuana use should disqualify an investigator from baptism is a different issue. Personally, I have no problem with using medical marijuana as long as some law permits it; this point of view is also shared by 89 percent of respondents to Wheat And Tares online poll. However, since neither Wheat And Tares nor I are General Authorities, our opinions are not authoritative. Those whose opinions are authoritative have spoken, and have said No. So be it. Any activism to change this is better directed towards changing the federal law; identify and support candidates for the U.S. Senate and House willing to decriminalize medical marijuana at the federal level.