Flash Game License has recently added an encryption service to the site. They have partnered with Kindisoft to bring this free encrytion service to your games. All you have to do is check a little box when uploading your game, and it will be fully encrypted as well as site-locked. The service is currently in beta, with a few bugs to work out. The service gives you the option of turning it on and off painlessly, so there are no worries of it permanently messing with your game. You can read more details about the service here.