I would leave the lights off, yes. There is no reason to suspect Malachite Green would help. Cardinals are notorious when it comes to troubles moving them. There probably isn't really anything you can do other then keep the stress levels as low as possible for a few days.
GL:
I don't think it is a good idea to add Cardinals to a newly cycled tank. They are very sensitive to nitrogen spikes. Newly cycled tanks are rarely stable and can throw small spikes for weeks after the fish are added as the bioloical filter adjusts to the new bio load.