You don't need to have the compressor on if the refrigerant level is so low as to lock it out. In that case the pressure in the filler can will be high enough to import refrigerant into the system. Go ahead and start the engine and turn the A/C on just as directed. The compressor will then start once the system charge is above the minimum for the compressor clutch to engage.
Have you already fixed whatever caused the low refrigerant level..?