When I got my Refrigerant Handling Certification from MACS many years ago, we were sworn to use a proper recycling machine, which captured everything and filtered out air, oils, and moisture. The refrigerant could then be re-used for the same or different vehicle. This was the transitional time, and there was much concern of a cheap "retrofit" DIY job creating a mix of R-12 "Freon" and R134a, which no machine could deal with.
When such contaminated refrigerant mixes were discovered, the offending stuff was shipped back to the manufacturer, or one of their agents, and destroyed - I know not by what manner - but I believe it was controlled incineration (Burning R-12 creates a sort of Mustard Gas) and that the process was very, very expensive. Most cases involved shipping and disposing of the "contaminated" recycling machine as well. I know many otherwise excellent and devout shops that illegally vented such systems, rather than incur a $10-$20k hazardous waste disposal incident. In truth, vacuuming for retrofit wasn't enough... there was always some residual chlorinated refrigerant stuck in the mineral oil, and the PAG oil wasn't sufficient viscosity to move it into solution.
Now with advent of R1234yf, this will eventually put me out of the A/C repair business. Whether it's flammable or not, as a shadetree independent I simply don't have the resources to buy yet another complete set of tools for dealing with the latest earth-friendly refrigerant.