If I were President and wanted to stop this, I think I could do it easily. I think it would make a lot of people mad, but I could do it, just like I could go start a big war in Syria if I wanted to.
If I were President and wanted to do this, I might do the following:
I could direct the DOJ to subpoena the records from every state of who is licensed to sell cannabis in that state. I might not have enough resources to prosecute them all at once, but I could direct the DOJ to raid and prosecute them one-by-one in no particular order. I could direct them to use late-night no-knock raids and (with plausible deniability) suggest that agents could shoot pets and cause extensive property damage with impunity. I could direct the DOJ to seize their assets under civil asset forfeiture, levy large fines, and imprison them for years, leaving their families destitute. I don't know if I would prosecute customers, but even if just a handful were prosecuted, it could have a huge chilling effect on legalization advocates. Finally, I could arrest and prosecute *all* state officials (whether elected or not) who had any part of administering the program.
By doing the above, I could intimidate both business and local government out of ever trying to legalize cannabis for decades to come.
I'm certain that the powers that be have thought about this, too.