If your new variable displacement compressor has a clutch (internally-controlled type), then go ahead. This type of compressor won't run even if the engine is running if the system is not charged, hence, no damage can occur. This is because the pressure switch shuts off the power supply to the compressor clutch preventing it from engaging. But just to sure, turn off the ac switch.
If your new compressor has no clutch (externally-controlled type), let me ask you these questions first:
1) Is the newly installed compressor a new one (fresh from the box)?
2) Is the oil in your compressor factory filled-in?
3) Did you flush your AC system?
If the answer to each of these questions is YES, then am against your driving your car for 50 miles to get it charged. The amount of oil that comes with the new compressor is so little and, with system flushed, could easily be dispersed out of the compressor, thus starving your compressor with the needed lubrication. Please note that a clutchless compressor is continuously running while the engine is running.