Rohrabacher-Farr has to be passed anew with each spending authorization and the current one expires later this month. If the administration decided they
really don't want it, they can go hard line on that, though there's political risk involved.
It explicitly also applies only to medical marijuana laws even as previously drafted; even if they don't go hardline against it they could either seek to have Congress revise it slightly to provide a clearer delineation of the medical boundary, or just go full-out against non-medical operations in recreational-use states and let the courts sort out the boundary; start a few RICO and/or Continuing Criminal Enterprise prosecutions with the associated broad forfeiture that can come with those (and the 20-year, or if your business is more successful, life) mandatory prison sentences available under the latter, and you'll drive lots of people that aren't yet being prosecuted out of “legal” pot and supporting businesses even before any legal challenges are resolved.
I respect Popehat a lot, but I think that while the minimization of the legal risk to individual users is accurate, it misses the real risk, which is to trade as a whole through selective targeting of major operations and supporting businesses. Individual users lose out because the “legal” industry goes away from legal risk, not because they are individually targeted for prosecution.