First, it is not true that no one goes to prison for mere possession. Mere possession of "too much" is automatically deemed to be for sale, even though no sale took place.
Secondly, until the sale is legal, the bad side effects will not stop. Growing and sale must be legal to put the black market out of business and make sure all the MJ cigarettes are made in factories with QA.
The government certainly knows this as well as anyone so we must make the normal assumption. "If you do not know why something is the way it is-It must be the money." There will be an economic upheaval in several industries when MJ is legalized: prison industry, drug testing and treatment, beer, lawyers, black market sellers-all these will suffer large losses in employment. It follows that the pressure to keep it illegal comes from them and the puritan drug warriors are the useful idiots of drug prohibition.
Wow did you just get that quote from an ACLU blast fax?