There are multiple questions going on here. One has to do with protecting your assets (graphics, music, etc) and the other has to do with protecting access to your game - we don't want people playing who haven't paid for it, right?
Let me first discuss assets. The MIS files you found, they might be .pngs, .mp3, etc with a different extension. It is possible that the MIS is only there to throw you off and if you changed the extension to .png and opened it up with paint it would work fine. It is also possible that the assets are heavily encrypted and very hard to grab without some type of decryption key. You can encrypt graphics and have your client decrypt them when they are used this way it becomes harder to steal your content. This is not a feature I am going to include in Intersect. Yes, I understand resources are very valuable but I am also a firm believer that if anyone is going to start their project by stealing your work then they don't have the resolve to actually get their project out there. I also know that dealing with encryption and decryption of assets during game design is a major hassle and a big pain in the arse for developers and users alike.
Now let's discuss access to your game. By default anyone with the .exe and resources can create an account and play. This means that your concern of someone making a copy via usb drive and distributing to their friends is a valid one. If you were charging per copy of your game then you could very easily be losing money with this design. The best solution I have to offer is to have a developer pull in some steam components into your client and server when the source is released. That way all in-game users have steam accounts and they would be checked to make sure they own the game upon signing in/creating a character. Having a system like that with a central authority like steam someone cannot share the game with others without fully giving up their account. There are other ways to accomplish this too. One terrible method would be to "trap" all new members on a map until you verify that they have paid and then warp them into the actual game world. On the other hand, you could create some other type of membership/authentication system completely to suit your needs. This is something else that we are not going to work on for the initial Intersect release. There are so many different platforms and ways to handle purchases. A lot of games will be free to play, other games will try to collect profit whether it is from selling the game itself or in-game transactions. Everyone will have a specific system they need and we cannot provide nor support them all. We will let those trying to monetize their game do so by hiring a programmer or coding it themselves to make it work however they'd like. We will make sure free to play platforms work well