If I remember correctly, Nixon's War on Drugs and the formation of the DEA was in response to the previous mechanism of making marijuana illegal (a catch-22 tax act) was ruled unconstitutional in the Supreme Court. So, I think it would really be a matter of whether RFK would care enough in 1968 to go through the motions of setting up a new system to keep weed (and other drugs) illegal.
Personally, I don't think he would. America in 1968 has bigger problems than hippies getting high, and RFK knows that. If he did, though, I can't see it being the same system Nixon used; it would probably look more like the decriminalization/tax and regulate system that NORML advocated for (and still does) OTL.