as long as your filters will still function properly with the tank lowered to 50 gallons, then i would suggest that. lower water level will also cause your filters to splash more, which in turn will raise the amount of oxygen being pushed into the water, which is a good thing when medicating and stressing fish IMO.
be sure to do really good gravel vacuuming during your water changes, as this will help to remove the bad bacteria down there that is causing the problems with the cories.